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protocols::cyclic_peptide::PeptideStubMover Class Reference

#include <PeptideStubMover.hh>

Inheritance diagram for protocols::cyclic_peptide::PeptideStubMover:
Inheritance graph
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Public Member Functions

 PeptideStubMover ()
 
 ~PeptideStubMover () override
 
 PeptideStubMover (PeptideStubMover const &src)
 
void init ()
 
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 reset_mover_data ()
 Reset mover data. More...
 
void set_reset_mode (bool reset_mode)
 Sets whether the pose gets reset (i.e. all residues deleted) or not. More...
 
void set_update_pdb_numbering_mode (bool mode)
 Sets whether pdb numbering gets updated or not. More...
 
void add_residue (std::string const &stubmode, std::string const &resname, core::Size const position, bool const jumpmode, std::string const &connecting_atom, core::Size const repeat, core::Size const anchor_rsd, core::select::residue_selector::ResidueSelectorCOP anchor_rsd_selector, std::string const &anchor_atom)
 Adds a residue to the list of residues to be appended, prepended, or inserted. More...
 
void add_residue (PSM_StubMode const stubmode, std::string const &resname, core::Size const position, bool const jumpmode, std::string const &connecting_atom, core::Size const repeat, core::Size const anchor_rsd, core::select::residue_selector::ResidueSelectorCOP anchor_rsd_selector, std::string const &anchor_atom)
 Adds a residue to the list of residues to be appended, prepended, or inserted. More...
 
std::string get_name () const override
 Each derived class must specify its name. The class name. More...
 
void set_residue_label (std::string const &label)
 add label to residues that are created with this mover 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...
 
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 std::string default_label ()
 
static void assign_chain_ids (core::pose::Pose &pose)
 
- 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

FirstResidAdded perform_single_iteration (core::pose::Pose &pose, core::chemical::ResidueTypeSet const &standard_residues, core::Size istub)
 this performs the inner loop logic of apply() More...
 
void handle_termini_and_store_terminal_dihedrals (core::pose::Pose &pose, core::Size const anchor_rsd, core::Size const istub, core::Size const connecting_id, core::Size &anchor_connecting_id, core::Real &old_omega_minus1, core::Real &old_phi, core::Real &old_psi, core::Real &old_omega, bool &replace_upper_terminal_type, bool &replace_lower_terminal_type)
 this function performs the early logic of append_by_bond() More...
 
core::Size get_connecting_id_for_append_by_bond (core::conformation::Residue const &new_rsd, core::Size const istub)
 determine how residues should connect when being appended by bond More...
 
FirstResidAdded append_by_jump (core::pose::Pose &pose, core::Size const anchor_rsd, core::conformation::Residue &new_rsd, core::Size const istub)
 Handle the case where the new residues start a new chain. More...
 
FirstResidAdded add_residue_to_empty_pose (core::pose::Pose &pose, core::conformation::Residue &new_rsd, core::Size const istub)
 Handle the case where the input pose has zero residues. More...
 
core::Size get_anchor_rsd (core::pose::Pose const &pose, core::Size const istub)
 queries stub_anchor_rsd_ and anchor_rsd_selectors_ to find the residue to use as an achor More...
 
FirstResidAdded append_by_bond (core::pose::Pose &pose, core::Size const anchor_rsd, core::conformation::Residue &new_rsd, core::Size const istub)
 returns resid of new residue More...
 
void handle_repeats_in_append_by_bond (core::pose::Pose &pose, core::Size const anchor_rsd, core::conformation::Residue &new_rsd, core::Size const istub)
 add additional residues if needed 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...
 

Private Member Functions

void handle_upper_terminus (core::pose::Pose &pose, core::Size const anchor_rsd, core::Real &old_psi, core::Real &old_omega, bool &replace_upper_terminal_type) const
 Remove terminal types from the upper terminus. Store the old psi and omega values. More...
 
void handle_lower_terminus (core::pose::Pose &pose, core::Size const anchor_rsd, core::Real &old_phi, core::Real &old_omega_nminus1, bool &replace_lower_terminal_type) const
 Remove terminal types from the lower terminus. Store the old phi and omega_nminus1 values. More...
 
void preserve_old_mainchain_torsions (core::pose::Pose &pose, core::Size const anchor_res, core::Real const old_omega_minus1, core::Real const old_phi, core::Real const old_psi, core::Real const old_omega, bool const replace_upper_terminal_type, bool const replace_lower_terminal_type) const
 Update the omega-1 and phi (if we've replaced an N-acetylation) or the psi and omega (if we've replaced a C-methylamidation) to preserve these dihedral values. More...
 
virtual void rebuild_atoms (core::pose::Pose &pose, core::Size const residue_index) const
 Rebuilds all atoms that are dependent on bonds between residue_index and any other residues (including atoms on the other residues). More...
 
void update_pdb_numbering (core::pose::Pose &pose, utility::vector1< core::Size > &resids_that_we_added) const
 Updates the PDB numbering (PDB number/chain ID) as residues are added. More...
 

Private Attributes

bool reset_
 
bool update_pdb_numbering_
 As residues are added, should the PDB numbering be updated? Default true. More...
 
utility::vector1< PSM_StubModestub_mode_
 
utility::vector1< std::string > stub_rsd_names_
 
utility::vector1< boolstub_rsd_jumping_
 
utility::vector1< std::string > stub_rsd_connecting_atom_
 
utility::vector1< core::Sizestub_rsd_repeat_
 
utility::vector1< core::Sizestub_insert_pos_
 
utility::vector1< core::Sizestub_anchor_rsd_
 
utility::vector1
< core::select::residue_selector::ResidueSelectorCOP
anchor_rsd_selectors_
 
utility::vector1< std::string > stub_anchor_rsd_connecting_atom_
 
std::string residue_label_ = DEFAULT_LABEL
 

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
 

Constructor & Destructor Documentation

protocols::cyclic_peptide::PeptideStubMover::PeptideStubMover ( )

References core::init::init().

protocols::cyclic_peptide::PeptideStubMover::~PeptideStubMover ( )
overridedefault
protocols::cyclic_peptide::PeptideStubMover::PeptideStubMover ( PeptideStubMover const &  src)
default

Member Function Documentation

void protocols::cyclic_peptide::PeptideStubMover::add_residue ( std::string const &  stubmode,
std::string const &  resname,
core::Size const  position,
bool const  jumpmode,
std::string const &  connecting_atom,
core::Size const  repeat,
core::Size const  anchor_rsd,
core::select::residue_selector::ResidueSelectorCOP  anchor_rsd_selector,
std::string const &  anchor_atom 
)

Adds a residue to the list of residues to be appended, prepended, or inserted.

Calls add_residue() override that uses PSM_StubMode.

References protocols::cyclic_peptide::PSM_append, protocols::cyclic_peptide::PSM_insert, and protocols::cyclic_peptide::PSM_prepend.

void protocols::cyclic_peptide::PeptideStubMover::add_residue ( PSM_StubMode const  stubmode,
std::string const &  resname,
core::Size const  position,
bool const  jumpmode,
std::string const &  connecting_atom,
core::Size const  repeat,
core::Size const  anchor_rsd,
core::select::residue_selector::ResidueSelectorCOP  anchor_rsd_selector,
std::string const &  anchor_atom 
)

Adds a residue to the list of residues to be appended, prepended, or inserted.

This version uses enums.

Author
Vikram K. Mulligan (vmull.nosp@m.ig@u.nosp@m.w.edu).

References protocols::cyclic_peptide::PSM_append, protocols::cyclic_peptide::PSM_insert, and protocols::cyclic_peptide::PSM_prepend.

FirstResidAdded protocols::cyclic_peptide::PeptideStubMover::add_residue_to_empty_pose ( core::pose::Pose pose,
core::conformation::Residue new_rsd,
core::Size const  istub 
)
protected

Handle the case where the input pose has zero residues.

Handle the case where the input pose has zero residues returns resid of the first new residue.

Returns
returns resid of the first new residue

References core::pose::Pose::append_residue_by_bond(), core::pose::Pose::append_residue_by_jump(), and protocols::cyclic_peptide::PSM_append.

FirstResidAdded protocols::cyclic_peptide::PeptideStubMover::append_by_bond ( core::pose::Pose pose,
core::Size const  anchor_rsd,
core::conformation::Residue new_rsd,
core::Size const  istub 
)
protected
FirstResidAdded protocols::cyclic_peptide::PeptideStubMover::append_by_jump ( core::pose::Pose pose,
core::Size const  anchor_rsd,
core::conformation::Residue new_rsd,
core::Size const  istub 
)
protected

Handle the case where the new residues start a new chain.

Handle the case where the new residues start a new chain returns resid of the first new residue added.

Returns
returns resid of the first new residue added

References core::pose::Pose::append_residue_by_bond(), core::pose::Pose::append_residue_by_jump(), protocols::cyclic_peptide::PSM_append, and core::pose::Pose::size().

void protocols::cyclic_peptide::PeptideStubMover::apply ( Pose )
overridevirtual
void protocols::cyclic_peptide::PeptideStubMover::assign_chain_ids ( core::pose::Pose pose)
static
moves::MoverOP protocols::cyclic_peptide::PeptideStubMover::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.

static std::string protocols::cyclic_peptide::PeptideStubMover::default_label ( )
inlinestatic
moves::MoverOP protocols::cyclic_peptide::PeptideStubMover::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.

core::Size protocols::cyclic_peptide::PeptideStubMover::get_anchor_rsd ( core::pose::Pose const &  pose,
core::Size const  istub 
)
protected

queries stub_anchor_rsd_ and anchor_rsd_selectors_ to find the residue to use as an achor

Returns
resid of anchor residue residue

References protocols::cyclic_peptide::PSM_prepend, core::select::resids(), and core::pose::Pose::size().

core::Size protocols::cyclic_peptide::PeptideStubMover::get_connecting_id_for_append_by_bond ( core::conformation::Residue const &  new_rsd,
core::Size const  istub 
)
protected
std::string protocols::cyclic_peptide::PeptideStubMover::get_name ( ) const
overridevirtual

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

Implements protocols::moves::Mover.

void protocols::cyclic_peptide::PeptideStubMover::handle_lower_terminus ( core::pose::Pose pose,
core::Size const  anchor_rsd,
core::Real old_phi,
core::Real old_omega_nminus1,
bool replace_lower_terminal_type 
) const
private

Remove terminal types from the lower terminus. Store the old phi and omega_nminus1 values.

Returns
Returns void, but if a terminal type was removed, old_phi will be set to the previous phi value and old_omega_nminus1 will be set to the previous upstream omega value. The replace_lower_terminal_type var is set to true if a terminal type was replaced and false otherwise.
Author
Vikram K. Mulligan (vmull.nosp@m.igan.nosp@m.@flat.nosp@m.iron.nosp@m.insti.nosp@m.tute.nosp@m..org).

References core::pose::Pose::conformation(), core::chemical::CUTPOINT_UPPER, core::chemical::ResidueTypeBase::has_variant_type(), core::chemical::ResidueType::is_alpha_aa(), core::chemical::ResidueType::is_beta_aa(), core::chemical::ResidueTypeBase::is_peptoid(), core::chemical::ResidueType::is_upper_terminus(), core::chemical::N_ACETYLATION, core::pose::Pose::phi(), core::pose::remove_upper_terminus_type_from_pose_residue(), core::pose::remove_variant_type_from_pose_residue(), core::pose::Pose::residue_type(), and core::conformation::Conformation::torsion_angle().

void protocols::cyclic_peptide::PeptideStubMover::handle_repeats_in_append_by_bond ( core::pose::Pose pose,
core::Size const  anchor_rsd,
core::conformation::Residue new_rsd,
core::Size const  istub 
)
protected
void protocols::cyclic_peptide::PeptideStubMover::handle_termini_and_store_terminal_dihedrals ( core::pose::Pose pose,
core::Size const  anchor_rsd,
core::Size const  istub,
core::Size const  connecting_id,
core::Size anchor_connecting_id,
core::Real old_omega_minus1,
core::Real old_phi,
core::Real old_psi,
core::Real old_omega,
bool replace_upper_terminal_type,
bool replace_lower_terminal_type 
)
protected
void protocols::cyclic_peptide::PeptideStubMover::handle_upper_terminus ( core::pose::Pose pose,
core::Size const  anchor_rsd,
core::Real old_psi,
core::Real old_omega,
bool replace_upper_terminal_type 
) const
private

Remove terminal types from the upper terminus. Store the old psi and omega values.

Returns
Returns void, but if a terminal type was removed, old_psi will be set to the previous psi value and old_omega will be set to the previous omega value. The replace_upper_terminal_type var is set to true if a terminal type was replaced and false otherwise.
Author
Vikram K. Mulligan (vmull.nosp@m.igan.nosp@m.@flat.nosp@m.iron.nosp@m.insti.nosp@m.tute.nosp@m..org).

References core::chemical::C_METHYLAMIDATION, core::chemical::CUTPOINT_LOWER, core::chemical::ResidueTypeBase::has_variant_type(), core::chemical::ResidueType::is_alpha_aa(), core::chemical::ResidueType::is_beta_aa(), core::chemical::ResidueTypeBase::is_peptoid(), core::chemical::ResidueType::is_upper_terminus(), core::pose::Pose::omega(), core::pose::Pose::psi(), core::pose::remove_upper_terminus_type_from_pose_residue(), core::pose::remove_variant_type_from_pose_residue(), and core::pose::Pose::residue_type().

void protocols::cyclic_peptide::PeptideStubMover::init ( void  )
std::string protocols::cyclic_peptide::PeptideStubMover::mover_name ( )
static
void protocols::cyclic_peptide::PeptideStubMover::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 core::select::residue_selector::parse_residue_selector().

FirstResidAdded protocols::cyclic_peptide::PeptideStubMover::perform_single_iteration ( core::pose::Pose pose,
core::chemical::ResidueTypeSet const &  standard_residues,
core::Size  istub 
)
protected

this performs the inner loop logic of apply()

returns resid

Returns
returns resid of the first new residue

References core::conformation::ResidueFactory::create_residue(), core::import_pose::get_anchor_rsd(), core::chemical::ResidueTypeSet::name_map(), and core::pose::Pose::size().

void protocols::cyclic_peptide::PeptideStubMover::preserve_old_mainchain_torsions ( core::pose::Pose pose,
core::Size const  anchor_res,
core::Real const  old_omega_minus1,
core::Real const  old_phi,
core::Real const  old_psi,
core::Real const  old_omega,
bool const  replace_upper_terminal_type,
bool const  replace_lower_terminal_type 
) const
private
void protocols::cyclic_peptide::PeptideStubMover::provide_xml_schema ( utility::tag::XMLSchemaDefinition &  xsd)
static
void protocols::cyclic_peptide::PeptideStubMover::rebuild_atoms ( core::pose::Pose pose,
core::Size const  residue_index 
) const
privatevirtual
void protocols::cyclic_peptide::PeptideStubMover::reset_mover_data ( )
inline
void protocols::cyclic_peptide::PeptideStubMover::set_reset_mode ( bool  reset_mode)
inline
void protocols::cyclic_peptide::PeptideStubMover::set_residue_label ( std::string const &  label)
inline

add label to residues that are created with this mover

Author
Jack Maguire, jackm.nosp@m.agui.nosp@m.re144.nosp@m.4@gm.nosp@m.ail.c.nosp@m.om

References residue_label_.

void protocols::cyclic_peptide::PeptideStubMover::set_update_pdb_numbering_mode ( bool  mode)
inline

Sets whether pdb numbering gets updated or not.

References update_pdb_numbering_.

void protocols::cyclic_peptide::PeptideStubMover::update_pdb_numbering ( core::pose::Pose pose,
utility::vector1< core::Size > &  resids_that_we_added 
) const
private

Updates the PDB numbering (PDB number/chain ID) as residues are added.

References core::pose::Pose::pdb_info(), and core::pose::Pose::size().

Member Data Documentation

utility::vector1<core::select::residue_selector::ResidueSelectorCOP> protocols::cyclic_peptide::PeptideStubMover::anchor_rsd_selectors_
private
bool protocols::cyclic_peptide::PeptideStubMover::reset_
private

Referenced by set_reset_mode().

std::string protocols::cyclic_peptide::PeptideStubMover::residue_label_ = DEFAULT_LABEL
private

Referenced by set_residue_label().

utility::vector1<core::Size> protocols::cyclic_peptide::PeptideStubMover::stub_anchor_rsd_
private

Referenced by reset_mover_data().

utility::vector1<std::string> protocols::cyclic_peptide::PeptideStubMover::stub_anchor_rsd_connecting_atom_
private

Referenced by reset_mover_data().

utility::vector1<core::Size> protocols::cyclic_peptide::PeptideStubMover::stub_insert_pos_
private
utility::vector1<PSM_StubMode> protocols::cyclic_peptide::PeptideStubMover::stub_mode_
private
utility::vector1<std::string> protocols::cyclic_peptide::PeptideStubMover::stub_rsd_connecting_atom_
private

Referenced by reset_mover_data().

utility::vector1<bool> protocols::cyclic_peptide::PeptideStubMover::stub_rsd_jumping_
private

Referenced by reset_mover_data().

utility::vector1<std::string> protocols::cyclic_peptide::PeptideStubMover::stub_rsd_names_
private

Referenced by reset_mover_data().

utility::vector1<core::Size> protocols::cyclic_peptide::PeptideStubMover::stub_rsd_repeat_
private
bool protocols::cyclic_peptide::PeptideStubMover::update_pdb_numbering_
private

As residues are added, should the PDB numbering be updated? Default true.

Referenced by set_update_pdb_numbering_mode().


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