#include <PeptideStubMover.hh>

Inheritance diagram for protocols::cyclic_peptide::PeptideStubMover:

[legend]

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...

void	provide_citation_info (basic::citation_manager::CitationCollectionList &citations) const override
	Provide citations to the passed CitationCollectionList. 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 Strings &	info ()
	non-const accessor More...

virtual Strings const &	info () const
	const accessor 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_StubMode >	stub_mode_

utility::vector1< std::string >	stub_rsd_names_

utility::vector1< bool >	stub_rsd_jumping_

utility::vector1< std::string >	stub_rsd_connecting_atom_

utility::vector1< core::Size >	stub_rsd_repeat_

utility::vector1< core::Size >	stub_insert_pos_

utility::vector1< core::Size >	stub_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

◆ PeptideStubMover() [1/2]

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

References core::init::init().

◆ ~PeptideStubMover()

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

overridedefault

◆ PeptideStubMover() [2/2]

protocols::cyclic_peptide::PeptideStubMover::PeptideStubMover ( PeptideStubMover const & src )

default

Member Function Documentation

◆ add_residue() [1/2]

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.

◆ add_residue() [2/2]

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.

Referenced by protocols::helical_bundle::MakeBundleHelix::apply(), protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication::build_polymer(), and protocols::helical_bundle_predict::HelicalBundlePredictApplication::make_pose_from_sequence_file_contents().

◆ add_residue_to_empty_pose()

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 @eturns 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.

◆ append_by_bond()

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

returns resid of new residue

Returns: returns resid of the first new residue

References core::pose::Pose::append_polymer_residue_after_seqpos(), core::pose::Pose::append_residue_by_bond(), core::pose::Pose::insert_residue_by_bond(), core::pose::Pose::prepend_polymer_residue_before_seqpos(), protocols::cyclic_peptide::PSM_append, protocols::cyclic_peptide::PSM_insert, and protocols::cyclic_peptide::PSM_prepend.

◆ append_by_jump()

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 @eturns 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().

◆ apply()

void protocols::cyclic_peptide::PeptideStubMover::apply ( Pose & )

overridevirtual

Main Method.

Implements protocols::moves::Mover.

References core::pose::Pose::clear(), protocols::cyclic_peptide::dump_debug_output(), core::chemical::FULL_ATOM_t, protocols::mean_field::max(), core::pose::Pose::residue_type_set_for_pose(), and TR().

Referenced by protocols::helical_bundle::MakeBundleHelix::apply(), protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication::build_polymer(), and protocols::helical_bundle_predict::HelicalBundlePredictApplication::make_pose_from_sequence_file_contents().

◆ assign_chain_ids()

void protocols::cyclic_peptide::PeptideStubMover::assign_chain_ids ( core::pose::Pose & pose )

static

References core::pose::Pose::chain(), core::pose::PDBInfo::get_reslabels(), core::chemical::one_indexed_chr_chains(), core::pose::Pose::pdb_info(), core::select::resids(), and core::pose::PDBInfo::set_resinfo().

Referenced by protocols::helical_bundle::MakeBundle::apply().

◆ clone()

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.

◆ default_label()

static std::string protocols::cyclic_peptide::PeptideStubMover::default_label ( )

inlinestatic

References protocols::cyclic_peptide::DEFAULT_LABEL.

◆ fresh_instance()

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.

◆ get_anchor_rsd()

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().

◆ get_connecting_id_for_append_by_bond()

core::Size protocols::cyclic_peptide::PeptideStubMover::get_connecting_id_for_append_by_bond	(	core::conformation::Residue const &	new_rsd,
		core::Size const	istub
	)

protected

determine how residues should connect when being appended by bond

References core::conformation::Residue::atom_index(), core::chemical::ResidueType::lower_connect_id(), core::chemical::ResidueType::residue_connection_id_for_atom(), TR(), and core::conformation::Residue::type().

◆ get_name()

std::string protocols::cyclic_peptide::PeptideStubMover::get_name ( ) const

overridevirtual

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

Implements protocols::moves::Mover.

◆ handle_lower_terminus()

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::chemical::ResidueType::atom_index(), 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().

◆ handle_repeats_in_append_by_bond()

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

add additional residues if needed

References core::pose::Pose::append_polymer_residue_after_seqpos(), core::pose::Pose::append_residue_by_bond(), core::pose::Pose::prepend_polymer_residue_before_seqpos(), protocols::cyclic_peptide::PSM_append, protocols::cyclic_peptide::PSM_insert, protocols::cyclic_peptide::PSM_prepend, and TR().

◆ handle_termini_and_store_terminal_dihedrals()

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

this function performs the early logic of append_by_bond()

call handle_upper_terminus and handle_lower_terminus

References core::chemical::ResidueType::atom_index(), core::chemical::ResidueType::lower_connect_id(), protocols::cyclic_peptide::PSM_append, protocols::cyclic_peptide::PSM_prepend, core::chemical::ResidueType::residue_connection_id_for_atom(), core::pose::Pose::residue_type(), TR(), and core::chemical::ResidueType::upper_connect_id().

◆ handle_upper_terminus()

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().

◆ init()

void protocols::cyclic_peptide::PeptideStubMover::init ( void )

◆ mover_name()

std::string protocols::cyclic_peptide::PeptideStubMover::mover_name ( )

static

◆ parse_my_tag()

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().

◆ perform_single_iteration()

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().

◆ preserve_old_mainchain_torsions()

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

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.

Builds a temporary foldtree rooted on the alpha carbon of the anchor residue.

Author: Vikram K. Mulligan (vmull.nosp@m.igan.nosp@m.@flat.nosp@m.iron.nosp@m.insti.nosp@m.tute.nosp@m..org).

◆ provide_citation_info()

void protocols::cyclic_peptide::PeptideStubMover::provide_citation_info ( basic::citation_manager::CitationCollectionList & citations ) const

overridevirtual

Provide citations to the passed CitationCollectionList.

Reimplemented from protocols::moves::Mover.

◆ provide_xml_schema()

void protocols::cyclic_peptide::PeptideStubMover::provide_xml_schema ( utility::tag::XMLSchemaDefinition & xsd )

static

References protocols::moves::xsd_type_definition_w_attributes_and_repeatable_subelements().

◆ rebuild_atoms()

void protocols::cyclic_peptide::PeptideStubMover::rebuild_atoms	(	core::pose::Pose &	pose,
		core::Size const	residue_index
	)		const

privatevirtual

Rebuilds all atoms that are dependent on bonds between residue_index and any other residues (including atoms on the other residues).

References core::chemical::ICoorAtomID::atomno(), core::chemical::AtomICoor::build(), core::pose::Pose::conformation(), core::conformation::Residue::connect_map(), core::conformation::Residue::connection_incomplete(), core::chemical::ResConnID::connid(), core::conformation::Residue::icoor(), core::conformation::Residue::n_possible_residue_connections(), core::conformation::Residue::natoms(), core::chemical::ResConnID::resid(), core::pose::Pose::residue(), core::conformation::Residue::residue_connect_atom_index(), core::conformation::Conformation::set_xyz(), core::pose::Pose::size(), and core::chemical::AtomICoor::stub_atom().

◆ reset_mover_data()

void protocols::cyclic_peptide::PeptideStubMover::reset_mover_data ( )

inline

Reset mover data.

References stub_anchor_rsd_, stub_anchor_rsd_connecting_atom_, stub_rsd_connecting_atom_, stub_rsd_jumping_, and stub_rsd_names_.

Referenced by protocols::helical_bundle::MakeBundleHelix::apply(), and protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication::build_polymer().

◆ set_reset_mode()

void protocols::cyclic_peptide::PeptideStubMover::set_reset_mode ( bool reset_mode )

inline

Sets whether the pose gets reset (i.e. all residues deleted) or not.

References reset_.

Referenced by protocols::helical_bundle::MakeBundleHelix::apply(), protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication::build_polymer(), and protocols::helical_bundle_predict::HelicalBundlePredictApplication::make_pose_from_sequence_file_contents().

◆ set_residue_label()

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

References residue_label_.

◆ set_update_pdb_numbering_mode()

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_.

◆ 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

◆ anchor_rsd_selectors_

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

private

◆ reset_

bool protocols::cyclic_peptide::PeptideStubMover::reset_

private

Referenced by set_reset_mode().

◆ residue_label_

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

private

Referenced by set_residue_label().

◆ stub_anchor_rsd_

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

private

Referenced by reset_mover_data().

◆ stub_anchor_rsd_connecting_atom_

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

private

Referenced by reset_mover_data().

◆ stub_insert_pos_

utility::vector1<core::Size> protocols::cyclic_peptide::PeptideStubMover::stub_insert_pos_

private

◆ stub_mode_

utility::vector1<PSM_StubMode> protocols::cyclic_peptide::PeptideStubMover::stub_mode_

private

◆ stub_rsd_connecting_atom_

utility::vector1<std::string> protocols::cyclic_peptide::PeptideStubMover::stub_rsd_connecting_atom_

private

Referenced by reset_mover_data().

◆ stub_rsd_jumping_

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

private

Referenced by reset_mover_data().

◆ stub_rsd_names_

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

private

Referenced by reset_mover_data().

◆ stub_rsd_repeat_

utility::vector1<core::Size> protocols::cyclic_peptide::PeptideStubMover::stub_rsd_repeat_

private

◆ update_pdb_numbering_

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:

src/protocols/cyclic_peptide/PeptideStubMover.hh
src/protocols/cyclic_peptide/PeptideStubMover.cc

Public Member Functions

Static Public Member Functions

Protected Member Functions

Private Member Functions

Private Attributes

Additional Inherited Members

Constructor & Destructor Documentation

◆ PeptideStubMover() [1/2]

◆ ~PeptideStubMover()

◆ PeptideStubMover() [2/2]

Member Function Documentation

◆ add_residue() [1/2]

◆ add_residue() [2/2]

◆ add_residue_to_empty_pose()

◆ append_by_bond()

◆ append_by_jump()

◆ apply()

◆ assign_chain_ids()

◆ clone()

◆ default_label()

◆ fresh_instance()

◆ get_anchor_rsd()

◆ get_connecting_id_for_append_by_bond()

◆ get_name()

◆ handle_lower_terminus()

◆ handle_repeats_in_append_by_bond()

◆ handle_termini_and_store_terminal_dihedrals()

◆ handle_upper_terminus()

◆ init()

◆ mover_name()

◆ parse_my_tag()

◆ perform_single_iteration()

◆ preserve_old_mainchain_torsions()

◆ provide_citation_info()

◆ provide_xml_schema()

◆ rebuild_atoms()

◆ reset_mover_data()

◆ set_reset_mode()

◆ set_residue_label()

◆ set_update_pdb_numbering_mode()

◆ update_pdb_numbering()

Member Data Documentation

◆ anchor_rsd_selectors_

◆ reset_

◆ residue_label_

◆ stub_anchor_rsd_

◆ stub_anchor_rsd_connecting_atom_

◆ stub_insert_pos_

◆ stub_mode_

◆ stub_rsd_connecting_atom_

◆ stub_rsd_jumping_

◆ stub_rsd_names_

◆ stub_rsd_repeat_

◆ update_pdb_numbering_