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protocols::carbohydrates::CreateGlycanSequonMover Class Reference

Mutates residues to create a potential glycosylation site using known sequence motifs of N- or C- linked glycans. Includes options for Enhanced Sequons for N-linked glycans that have been shown to have higher rates of glycosylation as well as other positions that have been shown to influence the glycosylation chemistry. More...

#include <CreateGlycanSequonMover.hh>

Inheritance diagram for protocols::carbohydrates::CreateGlycanSequonMover:
Inheritance graph
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Public Member Functions

 CreateGlycanSequonMover ()
 Constructors ///. More...
 
 CreateGlycanSequonMover (core::select::residue_selector::ResidueSelectorCOP selector)
 
 CreateGlycanSequonMover (CreateGlycanSequonMover const &src)
 Copy constructor (not needed unless you need deep copies) More...
 
 ~CreateGlycanSequonMover () override
 Destructor (important for properly forward-declaring smart-pointer members) More...
 
void apply (core::pose::Pose &pose) override
 Mover Methods ///. More...
 
bool mover_provides_citation_info () const override
 Does this mover provide information about how to cite it? More...
 
utility::vector1
< basic::citation_manager::UnpublishedModuleInfoCOP > 
provide_authorship_info_for_unpublished () const override
 Provide a list of authors and their e-mail addresses, as strings. More...
 
void set_glycosylation_position (core::Size position, core::pose::Pose const &pose)
 Set the target glycosylation position for which the sequence motif will be created around. If this is in beginning or end of protein and could not be created, will set fail do not retry mover status. More...
 
void set_residue_selector (core::select::residue_selector::ResidueSelectorCOP selector)
 Set a number of positions using a residue selector. The positions are where glycosylation is intended to occur. More...
 
void set_positions_as_start_of_sequon (bool positions_as_start)
 Instead of having each position be the glycosylation position, have each position be the start of the sequon. This just makes using ResidueSelectors with this class a bit easier if needed. More...
 
void set_use_basic_enhanced_n_linked_sequon (bool enhanced)
 Set to use the enhanced sequon which has been shown to result in higher rates of glycosylation and slightly lower complex types as the glycan site. (Aromatics at n+2) More...
 
void set_glycan_sequon_type (GlycanSequon sequon)
 Set any sequon type. More...
 
void set_score_function (core::scoring::ScoreFunctionCOP scorefxn)
 
void set_design_x_positions (bool const design_x_positions)
 If there is an X in the motif, should we design it or leave it alone. Default is to leave it alone. More...
 
void set_pack_rounds (core::Size pack_rounds)
 Number of rounds to run packing/design. Default is 5. More...
 
void set_pack_neighbors (bool const pack_neighbors)
 Should we pack neighbors of the motif? Default is True. More...
 
void set_design_neighbors (bool const design_neighbors)
 Should we design neighbors of the motif? Default is False. More...
 
void set_pack_distance (core::Real const pack_distance)
 Set the neighbor detection distance for any packing/design of neighbors. More...
 
void show (std::ostream &output=std::cout) const override
 Show the contents of the Mover. More...
 
void parse_my_tag (utility::tag::TagCOP tag, basic::datacache::DataMap &data) override
 Rosetta Scripts Support ///. More...
 
protocols::moves::MoverOP fresh_instance () const override
 required in the context of the parser/scripting scheme More...
 
protocols::moves::MoverOP clone () const override
 required in the context of the parser/scripting scheme More...
 
std::string get_name () const override
 Each derived class must specify its name. The class name. 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 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 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...
 

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

std::map< GlycanSequon,
std::string > 
sequons_
 
core::select::residue_selector::ResidueSelectorCOP selector_ = nullptr
 
GlycanSequon sequon_type_ = n_linked_typical
 
bool positions_as_start_of_sequon_ = false
 
bool design_x_positions_ = false
 
calc_taskop_movers::CreateSequenceMotifMoverOP motif_mover_
 
bool pack_neighbors_ = true
 
bool design_neighbors_ = false
 
core::Real pack_distance_ = 6.0
 
core::Size pack_rounds_ = 5
 
core::scoring::ScoreFunctionCOP scorefxn_ = nullptr
 

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...
 

Detailed Description

Mutates residues to create a potential glycosylation site using known sequence motifs of N- or C- linked glycans. Includes options for Enhanced Sequons for N-linked glycans that have been shown to have higher rates of glycosylation as well as other positions that have been shown to influence the glycosylation chemistry.

Creates the glycan sequence motif around (and including) the potential glycosylation site. If the site could not be created due to the position being too close to the beginning or end of the sequence, Will set the mover status to fail, do not retry.

Creates an N-Linked Sequence Motif by default using the non-enhanced motif. This can be changed in options.

Constructor & Destructor Documentation

protocols::carbohydrates::CreateGlycanSequonMover::CreateGlycanSequonMover ( )

Constructors ///.

Default constructor

References protocols::carbohydrates::create_sequons(), motif_mover_, and sequons_.

protocols::carbohydrates::CreateGlycanSequonMover::CreateGlycanSequonMover ( core::select::residue_selector::ResidueSelectorCOP  selector)
protocols::carbohydrates::CreateGlycanSequonMover::CreateGlycanSequonMover ( CreateGlycanSequonMover const &  src)

Copy constructor (not needed unless you need deep copies)

Copy constructor.

References protocols::carbohydrates::create_sequons(), motif_mover_, scorefxn_, selector_, and sequons_.

protocols::carbohydrates::CreateGlycanSequonMover::~CreateGlycanSequonMover ( )
override

Destructor (important for properly forward-declaring smart-pointer members)

Member Function Documentation

void protocols::carbohydrates::CreateGlycanSequonMover::apply ( core::pose::Pose pose)
overridevirtual

Mover Methods ///.

Apply the mover.

Apply the mover

If the sequon could not be created (for example the length of the sequon is longer than the protein/etc. It will set mover_failed_do_not retry. It is your responsiblity to catch this and do whatever you wish with it.

Implements protocols::moves::Mover.

References design_neighbors_, design_x_positions_, motif_mover_, protocols::carbohydrates::n_linked_basic_enhanced, protocols::carbohydrates::n_linked_best_enhanced, pack_distance_, pack_neighbors_, pack_rounds_, positions_as_start_of_sequon_, scorefxn_, selector_, sequon_type_, sequons_, core::id::to_string(), core::pose::Pose::total_residue(), and protocols::TR().

protocols::moves::MoverOP protocols::carbohydrates::CreateGlycanSequonMover::clone ( ) const
overridevirtual

required in the context of the parser/scripting scheme

Reimplemented from protocols::moves::Mover.

protocols::moves::MoverOP protocols::carbohydrates::CreateGlycanSequonMover::fresh_instance ( ) const
overridevirtual

required in the context of the parser/scripting scheme

Reimplemented from protocols::moves::Mover.

std::string protocols::carbohydrates::CreateGlycanSequonMover::get_name ( ) const
overridevirtual

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

Implements protocols::moves::Mover.

References mover_name().

std::string protocols::carbohydrates::CreateGlycanSequonMover::mover_name ( )
static
bool protocols::carbohydrates::CreateGlycanSequonMover::mover_provides_citation_info ( ) const
overridevirtual

Does this mover provide information about how to cite it?

Returns
true

Reimplemented from protocols::moves::Mover.

void protocols::carbohydrates::CreateGlycanSequonMover::parse_my_tag ( utility::tag::TagCOP  tag,
basic::datacache::DataMap &  data 
)
overridevirtual
utility::vector1< basic::citation_manager::UnpublishedModuleInfoCOP > protocols::carbohydrates::CreateGlycanSequonMover::provide_authorship_info_for_unpublished ( ) const
overridevirtual

Provide a list of authors and their e-mail addresses, as strings.

Reimplemented from protocols::moves::Mover.

References mover_name().

void protocols::carbohydrates::CreateGlycanSequonMover::provide_xml_schema ( utility::tag::XMLSchemaDefinition &  xsd)
static
void protocols::carbohydrates::CreateGlycanSequonMover::set_design_neighbors ( bool const  design_neighbors)

Should we design neighbors of the motif? Default is False.

References design_neighbors_.

Referenced by parse_my_tag().

void protocols::carbohydrates::CreateGlycanSequonMover::set_design_x_positions ( bool const  design_x_positions)

If there is an X in the motif, should we design it or leave it alone. Default is to leave it alone.

References design_x_positions_.

Referenced by parse_my_tag().

void protocols::carbohydrates::CreateGlycanSequonMover::set_glycan_sequon_type ( GlycanSequon  sequon)

Set any sequon type.

References sequon_type_.

void protocols::carbohydrates::CreateGlycanSequonMover::set_glycosylation_position ( core::Size  position,
core::pose::Pose const &  pose 
)

Set the target glycosylation position for which the sequence motif will be created around. If this is in beginning or end of protein and could not be created, will set fail do not retry mover status.

Mover Methods ///.

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

void protocols::carbohydrates::CreateGlycanSequonMover::set_pack_distance ( core::Real const  pack_distance)

Set the neighbor detection distance for any packing/design of neighbors.

References pack_distance_.

Referenced by parse_my_tag().

void protocols::carbohydrates::CreateGlycanSequonMover::set_pack_neighbors ( bool const  pack_neighbors)

Should we pack neighbors of the motif? Default is True.

References pack_neighbors_.

Referenced by parse_my_tag().

void protocols::carbohydrates::CreateGlycanSequonMover::set_pack_rounds ( core::Size  pack_rounds)

Number of rounds to run packing/design. Default is 5.

References pack_rounds_.

Referenced by parse_my_tag().

void protocols::carbohydrates::CreateGlycanSequonMover::set_positions_as_start_of_sequon ( bool  positions_as_start)

Instead of having each position be the glycosylation position, have each position be the start of the sequon. This just makes using ResidueSelectors with this class a bit easier if needed.

This only effects the basic_enhanced and best_enhanced sequons!

References positions_as_start_of_sequon_.

void protocols::carbohydrates::CreateGlycanSequonMover::set_residue_selector ( core::select::residue_selector::ResidueSelectorCOP  selector)

Set a number of positions using a residue selector. The positions are where glycosylation is intended to occur.

References selector_.

Referenced by CreateGlycanSequonMover(), and parse_my_tag().

void protocols::carbohydrates::CreateGlycanSequonMover::set_score_function ( core::scoring::ScoreFunctionCOP  scorefxn)

References scorefxn_.

Referenced by parse_my_tag().

void protocols::carbohydrates::CreateGlycanSequonMover::set_use_basic_enhanced_n_linked_sequon ( bool  enhanced)

Set to use the enhanced sequon which has been shown to result in higher rates of glycosylation and slightly lower complex types as the glycan site. (Aromatics at n+2)

DEFAULT: False

REFS: "Enhanced Aromatic Sequons Increase Oligosaccharyltransferase Glycosylation Efficiency and Glycan Homogeneity" Murray et al., 2015, Chemistry & Biology 22, 1052–1062 http://dx.doi.org/10.1016/j.chembiol.2015.06.017

"Residues Comprising the Enhanced Aromatic Sequon Influence Protein N‐Glycosylation Efficiency" Yen-Wen Huang, J. Am. Chem. Soc. 2017, 139, 12947−12955 DOI: 10.1021/jacs.7b03868

References protocols::carbohydrates::n_linked_basic_enhanced, protocols::carbohydrates::n_linked_typical, and sequon_type_.

void protocols::carbohydrates::CreateGlycanSequonMover::show ( std::ostream &  output = std::cout) const
overridevirtual

Show the contents of the Mover.

Reimplemented from protocols::moves::Mover.

References protocols::moves::Mover::show().

Referenced by protocols::carbohydrates::operator<<().

Member Data Documentation

bool protocols::carbohydrates::CreateGlycanSequonMover::design_neighbors_ = false
private
bool protocols::carbohydrates::CreateGlycanSequonMover::design_x_positions_ = false
private

Referenced by apply(), and set_design_x_positions().

calc_taskop_movers::CreateSequenceMotifMoverOP protocols::carbohydrates::CreateGlycanSequonMover::motif_mover_
private

Referenced by apply(), and CreateGlycanSequonMover().

core::Real protocols::carbohydrates::CreateGlycanSequonMover::pack_distance_ = 6.0
private
bool protocols::carbohydrates::CreateGlycanSequonMover::pack_neighbors_ = true
private
core::Size protocols::carbohydrates::CreateGlycanSequonMover::pack_rounds_ = 5
private
bool protocols::carbohydrates::CreateGlycanSequonMover::positions_as_start_of_sequon_ = false
private
core::scoring::ScoreFunctionCOP protocols::carbohydrates::CreateGlycanSequonMover::scorefxn_ = nullptr
private
core::select::residue_selector::ResidueSelectorCOP protocols::carbohydrates::CreateGlycanSequonMover::selector_ = nullptr
private
GlycanSequon protocols::carbohydrates::CreateGlycanSequonMover::sequon_type_ = n_linked_typical
private
std::map< GlycanSequon, std::string > protocols::carbohydrates::CreateGlycanSequonMover::sequons_
private

Referenced by apply(), and CreateGlycanSequonMover().


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