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protocols::carbohydrates::SimpleGlycosylateMover Class Reference

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:
Inheritance graph
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Public Member Functions

 SimpleGlycosylateMover ()
 
 SimpleGlycosylateMover (SimpleGlycosylateMover const &src)
 
 ~SimpleGlycosylateMover () override
 
void apply (core::pose::Pose &pose) override
 Main Method. 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 (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 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 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::Realglycosylation_weights_
 
utility::vector1< std::string > parsed_positions_
 
utility::vector1< core::Sizepositions_
 
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

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

References selector_.

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

Member Function Documentation

void protocols::carbohydrates::SimpleGlycosylateMover::apply ( core::pose::Pose )
overridevirtual
protocols::moves::MoverOP protocols::carbohydrates::SimpleGlycosylateMover::clone ( ) const
overridevirtual

required in the context of the parser/scripting scheme

Reimplemented from protocols::moves::Mover.

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

required in the context of the parser/scripting scheme

Reimplemented from protocols::moves::Mover.

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().

std::string protocols::carbohydrates::SimpleGlycosylateMover::mover_name ( )
static
bool protocols::carbohydrates::SimpleGlycosylateMover::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::SimpleGlycosylateMover::parse_my_tag ( utility::tag::TagCOP  tag,
basic::datacache::DataMap &  data 
)
overridevirtual
utility::vector1< basic::citation_manager::UnpublishedModuleInfoCOP > protocols::carbohydrates::SimpleGlycosylateMover::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::SimpleGlycosylateMover::provide_xml_schema ( utility::tag::XMLSchemaDefinition &  xsd)
static
void protocols::carbohydrates::SimpleGlycosylateMover::remove_index ( utility::vector1< core::Size > &  current_vector,
core::Size  resnum 
) const
private

Referenced by apply().

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_.

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_.

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_.

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

Set a single resnum position.

References positions_.

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

References positions_.

Referenced by apply().

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

Set positions from a Residue Selector.

References positions_, and selector_.

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_.

utility::vector1< std::string > protocols::carbohydrates::SimpleGlycosylateMover::setup_and_load_iupac_sequences ( ) const
private
void protocols::carbohydrates::SimpleGlycosylateMover::show ( std::ostream &  output = std::cout) const
overridevirtual

Outputs details about the Mover, including current settings.

Ideally, a child Mover should call Mover.show() and add additional information particular to that Mover.

Reimplemented from protocols::moves::Mover.

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

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

Member Data Documentation

utility::vector1< core::Real > protocols::carbohydrates::SimpleGlycosylateMover::glycosylation_weights_
private
utility::vector1< std::string > protocols::carbohydrates::SimpleGlycosylateMover::glycosylations_
private
bool protocols::carbohydrates::SimpleGlycosylateMover::idealize_glycosylation_
private

Referenced by apply(), and parse_my_tag().

utility::vector1< std::string > protocols::carbohydrates::SimpleGlycosylateMover::parsed_positions_
private

Referenced by apply(), and parse_my_tag().

utility::vector1< core::Size > protocols::carbohydrates::SimpleGlycosylateMover::positions_
private
std::string protocols::carbohydrates::SimpleGlycosylateMover::ref_pose_name_
private

Referenced by apply(), and parse_my_tag().

core::select::residue_selector::ResidueSelectorCOP protocols::carbohydrates::SimpleGlycosylateMover::selector_ = nullptr
private
bool protocols::carbohydrates::SimpleGlycosylateMover::strip_existing_glycans_
private

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