A mover for glycosylation of biological glycosylations. Currently glysolylation is done based on string, not from PDB. Use the GlycanSampler to model the resulting glycosylation!. More...

#include <SimpleGlycosylateMover.hh>

Inheritance diagram for protocols::carbohydrates::SimpleGlycosylateMover:

[legend]

Public Member Functions
	SimpleGlycosylateMover ()

	SimpleGlycosylateMover (SimpleGlycosylateMover const &src)

	~SimpleGlycosylateMover () override

void	apply (core::pose::Pose &pose) override
	Main Method. More...

void	provide_citation_info (basic::citation_manager::CitationCollectionList &) const override
	Provide the citation. More...

void	set_glycosylation (std::string const &iupac_or_common_string)
	Set the glycosylation that will happen. See database/chemical/carbohydrates/common_glycans for common names. Names include man3, man5, and man9. More...

void	set_glycosylations (utility::vector1< std::string > const &iupac_or_common_strings)
	Set possible glycosylations - the mover will randomly pick these on apply See database/chemical/carbohydrates/common_glycans for accepted names. Names include man3, man5, and man9. More...

void	set_position (core::Size position)
	Set a single resnum position. More...

void	set_residue_selector (core::select::residue_selector::ResidueSelectorCOP selector)
	Set positions from a Residue Selector. More...

void	set_glycosylation_weights (utility::vector1< core::Real > const &weights)
	Set weights for potential glycosylation if more than one is set. More...

void	set_strip_existing_glycans (bool strip_existing)
	This sets whether if we already have a glycan at a position, whether to extend it or delete the existing glycan. Advanced functionality - use with caution. Not yet work. More...

void	show (std::ostream &output=std::cout) const override
	Outputs details about the Mover, including current settings. More...

void	parse_my_tag (utility::tag::TagCOP tag, basic::datacache::DataMap &data) override
	parse XML tag (to use this Mover in Rosetta Scripts) More...

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 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 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 Member Functions
void	remove_index (utility::vector1< core::Size > &current_vector, core::Size resnum) const

utility::vector1< std::string >	setup_and_load_iupac_sequences () const

void	set_positions (utility::vector1< bool > const &positions)

Private Attributes
utility::vector1< std::string >	glycosylations_

utility::vector1< core::Real >	glycosylation_weights_

utility::vector1< std::string >	parsed_positions_

utility::vector1< core::Size >	positions_

utility::vector1< std::string >	parsed_atom_names_

boost::unordered_map< core::Size, std::string >	atom_names_

bool	strip_existing_glycans_

std::string	ref_pose_name_

bool	idealize_glycosylation_

core::select::residue_selector::ResidueSelectorCOP	selector_ = 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

A mover for glycosylation of biological glycosylations. Currently glysolylation is done based on string, not from PDB. Use the GlycanSampler to model the resulting glycosylation!.

Single Glycosylation: If a single glycosylation is passed, it will glycosylate all positions set with this glycan.

Multiple Glycosylations: If multiple glycosylations are passed, will randomly select from these on apply to sample glycan hetergenecity. see glyco.set_weights to set weights for these glycans to sample non-random heterogenecity in the glycoform.

The site should be ASN for N-linked glycosylations OR SER/THR for O-linked glycosylations If a glycan already exists, will strip off the current glycan by default. set glyco.set_strip_existing_glycans( false ) to branch off existing glycans instead of deleting them.

see CreateGlycoSiteMover to create glyco sites (as N-linked glycosylations will need a specific motif to be biological)

Will randomly select from set positions and glycosylate all positions set.

Glycosylations: 1) If your name ends with .iupac or .gws (GlycoWorkBench), will try to load the file

2) Next, it will check the short names in the Rosetta database for your string. If the string is in common_names.txt, will load the paired iupac sequence. See database/chemical/carbohydrates/common_glycans/common_names.txt for accepted short names. Names include man3, man5, and man9.

3) If the name is not found, will attempt to build the glycan as an iupac sequence from the string.

TODO JAB: Add Glycosylate from pdb/cif files in addition to IUPAC and short names. No current RosettaCarbohydrate functionality to load from PDB/CIF and attach to an existing pose..

Constructor & Destructor Documentation

◆ SimpleGlycosylateMover() [1/2]

protocols::carbohydrates::SimpleGlycosylateMover::SimpleGlycosylateMover ( )

◆ SimpleGlycosylateMover() [2/2]

protocols::carbohydrates::SimpleGlycosylateMover::SimpleGlycosylateMover ( SimpleGlycosylateMover const & src )

References selector_.

◆ ~SimpleGlycosylateMover()

protocols::carbohydrates::SimpleGlycosylateMover::~SimpleGlycosylateMover ( )

overridedefault

Member Function Documentation

◆ apply()

void protocols::carbohydrates::SimpleGlycosylateMover::apply ( core::pose::Pose & )

overridevirtual

◆ clone()

protocols::moves::MoverOP protocols::carbohydrates::SimpleGlycosylateMover::clone ( ) const

overridevirtual

required in the context of the parser/scripting scheme

Reimplemented from protocols::moves::Mover.

◆ fresh_instance()

moves::MoverOP protocols::carbohydrates::SimpleGlycosylateMover::fresh_instance ( ) const

overridevirtual

required in the context of the parser/scripting scheme

Reimplemented from protocols::moves::Mover.

◆ get_name()

std::string protocols::carbohydrates::SimpleGlycosylateMover::get_name ( ) const

overridevirtual

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

Implements protocols::moves::Mover.

References mover_name().

◆ mover_name()

std::string protocols::carbohydrates::SimpleGlycosylateMover::mover_name ( )

static

Referenced by get_name(), protocols::carbohydrates::SimpleGlycosylateMoverCreator::keyname(), provide_citation_info(), and provide_xml_schema().

◆ parse_my_tag()

void protocols::carbohydrates::SimpleGlycosylateMover::parse_my_tag	(	utility::tag::TagCOP	tag,
		basic::datacache::DataMap &	data
	)

overridevirtual

parse XML tag (to use this Mover in Rosetta Scripts)

Reimplemented from protocols::moves::Mover.

References atom_names_, glycosylation_weights_, glycosylations_, idealize_glycosylation_, core::select::residue_selector::parse_residue_selector(), parsed_atom_names_, parsed_positions_, positions_, ref_pose_name_, selector_, and strip_existing_glycans_.

◆ provide_citation_info()

void protocols::carbohydrates::SimpleGlycosylateMover::provide_citation_info ( basic::citation_manager::CitationCollectionList & citations ) const

overridevirtual

Provide the citation.

Reimplemented from protocols::moves::Mover.

References mover_name().

◆ provide_xml_schema()

void protocols::carbohydrates::SimpleGlycosylateMover::provide_xml_schema ( utility::tag::XMLSchemaDefinition & xsd )

static

References protocols::rosetta_scripts::attributes_for_parse_residue_selector(), mover_name(), protocols::docking::membrane::real_regex_pattern(), and protocols::moves::xsd_type_definition_w_attributes_and_repeatable_subelements().

Referenced by protocols::carbohydrates::SimpleGlycosylateMoverCreator::provide_xml_schema().

◆ remove_index()

void protocols::carbohydrates::SimpleGlycosylateMover::remove_index	(	utility::vector1< core::Size > &	current_vector,
		core::Size	resnum
	)		const

private

Referenced by apply().

◆ set_glycosylation()

void protocols::carbohydrates::SimpleGlycosylateMover::set_glycosylation ( std::string const & iupac_or_common_string )

Set the glycosylation that will happen. See database/chemical/carbohydrates/common_glycans for common names. Names include man3, man5, and man9.

Can also use full iupac names.

See also: glycosylate.set_glycosylation_weights

References glycosylations_.

◆ set_glycosylation_weights()

void protocols::carbohydrates::SimpleGlycosylateMover::set_glycosylation_weights ( utility::vector1< core::Real > const & weights )

Set weights for potential glycosylation if more than one is set.

References glycosylation_weights_.

◆ set_glycosylations()

void protocols::carbohydrates::SimpleGlycosylateMover::set_glycosylations ( utility::vector1< std::string > const & iupac_or_common_strings )

Set possible glycosylations - the mover will randomly pick these on apply See database/chemical/carbohydrates/common_glycans for accepted names. Names include man3, man5, and man9.

Can also use full iupac names.

See also: glycosylate.set_glycosylation_weights

References glycosylations_.

Referenced by protocols::glycopeptide_docking::glycosylate_residues().

◆ set_position()

void protocols::carbohydrates::SimpleGlycosylateMover::set_position ( core::Size position )

Set a single resnum position.

References positions_.

◆ set_positions()

void protocols::carbohydrates::SimpleGlycosylateMover::set_positions ( utility::vector1< bool > const & positions )

private

References positions_.

Referenced by apply().

◆ set_residue_selector()

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

Set positions from a Residue Selector.

References positions_, and selector_.

Referenced by protocols::glycopeptide_docking::glycosylate_residues().

◆ set_strip_existing_glycans()

void protocols::carbohydrates::SimpleGlycosylateMover::set_strip_existing_glycans ( bool strip_existing )

This sets whether if we already have a glycan at a position, whether to extend it or delete the existing glycan. Advanced functionality - use with caution. Not yet work.

References strip_existing_glycans_.