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protocols::cyclic_peptide::DeclareBond Class Reference

#include <DeclareBond.hh>

Inheritance diagram for protocols::cyclic_peptide::DeclareBond:
Inheritance graph
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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 Stringsinfo ()
 non-const accessor More...
 
virtual Strings const & info () const
 const accessor More...
 
virtual bool mover_provides_citation_info () const
 Does this mover provide information about how to cite it? More...
 
virtual utility::vector1
< basic::citation_manager::CitationCollectionCOP > 
provide_citation_info () const
 Provide the citation. More...
 
virtual bool mover_is_unpublished () const
 Does this mover indicate that it is unpublished (and, by extension, that the author should be included in publications resulting from it)? More...
 
virtual utility::vector1
< basic::citation_manager::UnpublishedModuleInfoCOP > 
provide_authorship_info_for_unpublished () const
 Provide a list of authors and their e-mail addresses, as strings. 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

protocols::cyclic_peptide::DeclareBond::DeclareBond ( )
protocols::cyclic_peptide::DeclareBond::~DeclareBond ( )
overridedefault

Member Function Documentation

void protocols::cyclic_peptide::DeclareBond::apply ( Pose )
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, core::chemical::ResidueType::n_possible_residue_connections(), 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::cyclic_peptide::TR(), core::pose::Pose::update_residue_neighbors(), core::chemical::ResidueType::upper_connect_id(), and core::chemical::UPPER_TERMINUS_VARIANT.

Referenced by protocols::cyclic_peptide::crosslinker::TBMB_Helper::add_linker_bonds_symmetric(), and protocols::cyclic_peptide::crosslinker::TMA_Helper::add_linker_bonds_symmetric().

moves::MoverOP protocols::cyclic_peptide::DeclareBond::clone ( ) const
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.

moves::MoverOP protocols::cyclic_peptide::DeclareBond::fresh_instance ( ) const
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.

std::string protocols::cyclic_peptide::DeclareBond::get_name ( ) const
overridevirtual

Each derived class must specify its name. The class name.

Implements protocols::moves::Mover.

References mover_name().

std::string protocols::cyclic_peptide::DeclareBond::mover_name ( )
static
void protocols::cyclic_peptide::DeclareBond::parse_my_tag ( utility::tag::TagCOP  tag,
basic::datacache::DataMap &  data 
)
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_.

void protocols::cyclic_peptide::DeclareBond::provide_xml_schema ( utility::tag::XMLSchemaDefinition &  xsd)
static
void protocols::cyclic_peptide::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 
)
void protocols::cyclic_peptide::DeclareBond::set_selector_for_res1 ( core::select::residue_selector::ResidueSelectorCOP  selector1)
inline

References selector1_.

void protocols::cyclic_peptide::DeclareBond::set_selector_for_res2 ( core::select::residue_selector::ResidueSelectorCOP  selector2)
inline

References selector2_.

Member Data Documentation

bool protocols::cyclic_peptide::DeclareBond::add_termini_
private

Referenced by apply(), parse_my_tag(), and set().

std::string protocols::cyclic_peptide::DeclareBond::atom1_
private

Referenced by apply(), parse_my_tag(), and set().

std::string protocols::cyclic_peptide::DeclareBond::atom2_
private

Referenced by apply(), parse_my_tag(), and set().

core::Size protocols::cyclic_peptide::DeclareBond::kic_res1_
private

Referenced by apply(), parse_my_tag(), and set().

core::Size protocols::cyclic_peptide::DeclareBond::kic_res2_
private

Referenced by apply(), parse_my_tag(), and set().

bool protocols::cyclic_peptide::DeclareBond::rebuild_fold_tree_
private

Should the foldtree be rebuilt?

Referenced by apply(), parse_my_tag(), and set().

core::Size protocols::cyclic_peptide::DeclareBond::res1_
private

Referenced by apply(), parse_my_tag(), and set().

core::Size protocols::cyclic_peptide::DeclareBond::res2_
private

Referenced by apply(), parse_my_tag(), and set().

bool protocols::cyclic_peptide::DeclareBond::run_kic_
private

Referenced by apply(), parse_my_tag(), and set().

core::select::residue_selector::ResidueSelectorCOP protocols::cyclic_peptide::DeclareBond::selector1_ = nullptr
private
core::select::residue_selector::ResidueSelectorCOP protocols::cyclic_peptide::DeclareBond::selector2_ = nullptr
private

The documentation for this class was generated from the following files: