#include <DeclareBond.hh>
Public Member Functions | |
| DeclareBond () | |
| ~DeclareBond () override | |
| void | apply (Pose &) override |
| Main Method. More... | |
| moves::MoverOP | clone () const override |
| Return a clone of the Mover object. More... | |
| moves::MoverOP | fresh_instance () const override |
| Generates a new Mover object freshly created with the default ctor. More... | |
| void | parse_my_tag (utility::tag::TagCOP, basic::datacache::DataMap &) override |
| parse XML (specifically in the context of the parser/scripting scheme) More... | |
| void | set (core::Size const res1, std::string const &atom1, core::Size const res2, std::string const &atom2, bool const add_termini, bool const run_kic=false, core::Size const kic_res1=0, core::Size const kic_res2=0, bool const rebuild_fold_tree=false) |
| std::string | get_name () const override |
| Each derived class must specify its name. The class name. More... | |
| void | set_selector_for_res1 (core::select::residue_selector::ResidueSelectorCOP selector1) |
| void | set_selector_for_res2 (core::select::residue_selector::ResidueSelectorCOP selector2) |
 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 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... | |
| 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 |
| 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... | |
Static Public Member Functions | |
| static std::string | mover_name () |
| static void | provide_xml_schema (utility::tag::XMLSchemaDefinition &xsd) |
| 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... | |
Private Attributes | |
| core::select::residue_selector::ResidueSelectorCOP | selector1_ = nullptr |
| core::Size | res1_ |
| std::string | atom1_ |
| core::select::residue_selector::ResidueSelectorCOP | selector2_ = nullptr |
| core::Size | res2_ |
| std::string | atom2_ |
| bool | add_termini_ |
| bool | run_kic_ |
| core::Size | kic_res1_ |
| core::Size | kic_res2_ |
| bool | rebuild_fold_tree_ |
| Should the foldtree be rebuilt? 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 |
| 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
◆ DeclareBond()
| protocols::simple_moves::DeclareBond::DeclareBond | ( | ) |
◆ ~DeclareBond()
|
overridedefault |
Member Function Documentation
◆ apply()
|
overridevirtual |
Main Method.
Implements protocols::moves::Mover.
References add_termini_, core::pose::add_variant_type_to_pose_residue(), core::pose::Pose::append_residue_by_bond(), core::pose::Pose::append_residue_by_jump(), atom1_, atom2_, core::chemical::ResidueType::atom_index(), core::pose::Pose::chain(), core::pose::Pose::clear(), core::pose::Pose::conformation(), core::conformation::Residue::connect_map(), core::conformation::Residue::connected_residue_at_lower(), core::conformation::Residue::connected_residue_at_resconn(), core::conformation::Residue::connected_residue_at_upper(), core::chemical::ResConnID::connid(), core::chemical::CUTPOINT_LOWER, core::chemical::CUTPOINT_UPPER, core::conformation::Conformation::declare_chemical_bond(), core::scoring::get_score_function(), core::conformation::Residue::has_variant_type(), core::chemical::ResidueType::is_alpha_aa(), core::chemical::ResidueType::is_beta_aa(), core::chemical::ResidueTypeBase::is_peptoid(), kic_res1_, kic_res2_, core::chemical::ResidueType::lower_connect_id(), core::chemical::LOWER_TERMINUS_VARIANT, rebuild_fold_tree_, core::conformation::Conformation::rebuild_polymer_bond_dependent_atoms_this_residue_only(), core::conformation::Conformation::rebuild_residue_connection_dependent_atoms(), core::pose::remove_variant_type_from_pose_residue(), res1_, res2_, core::pose::Pose::residue(), core::chemical::ResidueType::residue_connection_id_for_atom(), core::pose::Pose::residue_type(), run_kic_, selector1_, selector2_, core::conformation::Conformation::set_noncanonical_connection(), core::pose::Pose::size(), protocols::simple_moves::TR(), core::pose::Pose::update_residue_neighbors(), core::chemical::ResidueType::upper_connect_id(), and core::chemical::UPPER_TERMINUS_VARIANT.
Referenced by protocols::energy_based_clustering::EnergyBasedClusteringProtocol::add_cyclic_constraints(), protocols::cyclic_peptide::crosslinker::One_Four_BBMB_Helper::add_linker_bonds_asymmetric(), protocols::cyclic_peptide::crosslinker::TBMB_Helper::add_linker_bonds_asymmetric(), protocols::cyclic_peptide::crosslinker::Thioether_Helper::add_linker_bonds_asymmetric(), protocols::cyclic_peptide::crosslinker::TMA_Helper::add_linker_bonds_asymmetric(), protocols::cyclic_peptide::crosslinker::One_Four_BBMB_Helper::add_linker_bonds_symmetric(), protocols::cyclic_peptide::crosslinker::TBMB_Helper::add_linker_bonds_symmetric(), and protocols::cyclic_peptide::crosslinker::TMA_Helper::add_linker_bonds_symmetric().
◆ 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.
◆ 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_name()
|
overridevirtual |
Each derived class must specify its name. The class name.
Implements protocols::moves::Mover.
References mover_name().
◆ mover_name()
|
static |
Referenced by get_name(), protocols::simple_moves::DeclareBondCreator::keyname(), and provide_xml_schema().
◆ parse_my_tag()
|
overridevirtual |
parse XML (specifically in the context of the parser/scripting scheme)
Reimplemented from protocols::moves::Mover.
References add_termini_, atom1_, atom2_, kic_res1_, kic_res2_, core::select::residue_selector::parse_residue_selector(), rebuild_fold_tree_, res1_, res2_, run_kic_, selector1_, and selector2_.
◆ provide_xml_schema()
|
static |
◆ set()
| void protocols::simple_moves::DeclareBond::set | ( | core::Size const | res1, |
| std::string const & | atom1, | ||
| core::Size const | res2, | ||
| std::string const & | atom2, | ||
| bool const | add_termini, | ||
| bool const | run_kic = false, |
||
| core::Size const | kic_res1 = 0, |
||
| core::Size const | kic_res2 = 0, |
||
| bool const | rebuild_fold_tree = false |
||
| ) |
References add_termini_, atom1_, atom2_, kic_res1_, kic_res2_, rebuild_fold_tree_, res1_, res2_, and run_kic_.
Referenced by protocols::energy_based_clustering::EnergyBasedClusteringProtocol::add_cyclic_constraints(), protocols::cyclic_peptide::crosslinker::One_Four_BBMB_Helper::add_linker_bonds_asymmetric(), protocols::cyclic_peptide::crosslinker::TBMB_Helper::add_linker_bonds_asymmetric(), protocols::cyclic_peptide::crosslinker::TMA_Helper::add_linker_bonds_asymmetric(), protocols::cyclic_peptide::crosslinker::One_Four_BBMB_Helper::add_linker_bonds_symmetric(), protocols::cyclic_peptide::crosslinker::TBMB_Helper::add_linker_bonds_symmetric(), protocols::cyclic_peptide::crosslinker::TMA_Helper::add_linker_bonds_symmetric(), and protocols::cyclic_peptide::crosslinker::set_up_thioether_bond_mover().
◆ set_selector_for_res1()
|
inline |
References selector1_.
◆ set_selector_for_res2()
|
inline |
References selector2_.
Member Data Documentation
◆ add_termini_
|
private |
Referenced by apply(), parse_my_tag(), and set().
◆ atom1_
|
private |
Referenced by apply(), parse_my_tag(), and set().
◆ atom2_
|
private |
Referenced by apply(), parse_my_tag(), and set().
◆ kic_res1_
|
private |
Referenced by apply(), parse_my_tag(), and set().
◆ kic_res2_
|
private |
Referenced by apply(), parse_my_tag(), and set().
◆ rebuild_fold_tree_
|
private |
Should the foldtree be rebuilt?
Referenced by apply(), parse_my_tag(), and set().
◆ res1_
|
private |
Referenced by apply(), parse_my_tag(), and set().
◆ res2_
|
private |
Referenced by apply(), parse_my_tag(), and set().
◆ run_kic_
|
private |
Referenced by apply(), parse_my_tag(), and set().
◆ selector1_
|
private |
Referenced by apply(), parse_my_tag(), and set_selector_for_res1().
◆ selector2_
|
private |
Referenced by apply(), parse_my_tag(), and set_selector_for_res2().
The documentation for this class was generated from the following files:
- src/protocols/simple_moves/DeclareBond.hh
- src/protocols/simple_moves/DeclareBond.cc
