Public Member Functions | Static Public Member Functions | Private Member Functions | Private Attributes | List of all members
protocols::glycopeptide_docking::GlycopeptideDockingProtocol Class Reference

A protocol to predict glycosylation and elongation of glycans. More...

#include <GlycopeptideDockingProtocol.hh>

Inheritance diagram for protocols::glycopeptide_docking::GlycopeptideDockingProtocol:
Inheritance graph

Public Member Functions

 GlycopeptideDockingProtocol ()
 Constructors ///. More...
 GlycopeptideDockingProtocol (GlycopeptideDockingFlags &flags)
 Constructor with flags. More...
 GlycopeptideDockingProtocol (GlycopeptideDockingProtocol const &object_to_copy)
 Copy constructor (not needed unless you need deep copies) More...
GlycopeptideDockingProtocoloperator= (GlycopeptideDockingProtocol const &object_to_copy)
 Assignment operator. More...
 ~GlycopeptideDockingProtocol () override
 Destructor (important for properly forward-declaring smart-pointer members) More...
void apply (core::pose::Pose &pose) override
 Mover Methods ///. More...
void show (std::ostream &output=std::cout) const override
 Show mover information. More...
void set_ref_pose_from_filename (std::string const &filename)
 Set reference pose (native) from file name. 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 void provide_citation_info (basic::citation_manager::CitationCollectionList &) const
 Provide citations to the passed CitationCollectionList Subclasses should add the info for themselves and any other classes they use. 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 copy_data (GlycopeptideDockingProtocol &object_to_copy_to, GlycopeptideDockingProtocol const &object_to_copy_from)
 Copy protocol data. More...
void prepare_score_function ()
 Prepare scorefunction. Currently the scorefunction is fixed by design. Benchmarking has not been done with other scorefunctions. More...

Private Attributes

protocols::glycopeptide_docking::GlycopeptideDockingFlagsOP flags_
core::scoring::ScoreFunctionOP sf_
protocols::moves::MonteCarloOP mc_
protocols::constraint_movers::ConstraintSetMoverOP constraint_setter_
core::pose::PoseOP ref_pose_ =nullptr
core::kinematics::FoldTreeOP ft_docking_ =nullptr
core::kinematics::FoldTreeOP ft_substrate_ =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 protocol to predict glycosylation and elongation of glycans.

This protocol is intended to "sample" glycopeptide poses/conformations in the context of the glycosyltransferase "ready" to be glycosylated. Similar to enzyme-design protocols, constraints can be specified to emulate the positioning of atoms/residues in the transition state comingsoon(3-4 months): We are currently prototyping an extension to generalize the protocol for elongation to core1, core2 and higher sugars with their respective glcyosyltransferases. We hope to automate substrate generation from peptide-sequence and glycosylation (for glycopeptide substrates), donor glycosylation (e.g. UDP->UDP-Sugar) and initial setup of the peptide-substrate in the active site. Additional options are defined in GlycopeptideDockingFlags.hh

Constructor & Destructor Documentation

◆ GlycopeptideDockingProtocol() [1/3]

protocols::glycopeptide_docking::GlycopeptideDockingProtocol::GlycopeptideDockingProtocol ( )

Constructors ///.

Default constructor

References constraint_setter_, flags_, prepare_score_function(), and protocols::moves::Mover::type().

◆ GlycopeptideDockingProtocol() [2/3]

protocols::glycopeptide_docking::GlycopeptideDockingProtocol::GlycopeptideDockingProtocol ( GlycopeptideDockingFlags flags)

Constructor with flags.

Constructor with flags object as argument.

References constraint_setter_, flags_, prepare_score_function(), and protocols::moves::Mover::type().

◆ GlycopeptideDockingProtocol() [3/3]

protocols::glycopeptide_docking::GlycopeptideDockingProtocol::GlycopeptideDockingProtocol ( GlycopeptideDockingProtocol const &  object_to_copy)

Copy constructor (not needed unless you need deep copies)

Copy constructor.

References copy_data().

◆ ~GlycopeptideDockingProtocol()

protocols::glycopeptide_docking::GlycopeptideDockingProtocol::~GlycopeptideDockingProtocol ( )

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

Member Function Documentation

◆ apply()

void protocols::glycopeptide_docking::GlycopeptideDockingProtocol::apply ( core::pose::Pose pose)

Mover Methods ///.

Apply the mover

Apply 1. Setups sampling options that require pose, including setting up glycosylation fold tree, substrate and enzyme chains. If user specifies residues to be preglycosylated before sampling, apply does it. 2. Randomizes peptide backbone torsions if requested.

  1. Runs low-resolution sampling of peptide/glycopeptide-enzyme if enabled. 4. Runs high-resolution of peptide/glycopeptide-enzyme of enabled. 5. Records metrics.

Implements protocols::moves::Mover.

References protocols::glycopeptide_docking::GlycopeptideDockingHighResRefinement::apply(), protocols::glycopeptide_docking::GlycopeptideDockingLowResRefinement::apply(), constraint_setter_, flags_, core::pose::Pose::fold_tree(), ft_docking_, ft_substrate_, protocols::jd2::JobDistributor::get_instance(), protocols::glycopeptide_docking::record_pose_metrics(), ref_pose_, core::scoring::rg, core::pose::Pose::set_phi(), core::pose::Pose::set_psi(), protocols::glycopeptide_docking::setup_glycosylation_foldtree(), sf_, protocols::glycopeptide_docking::GlycopeptideDockingHighResRefinement::show(), protocols::TR(), and protocols::glycopeptide_docking::write_debug_pdb().

◆ clone()

protocols::moves::MoverOP protocols::glycopeptide_docking::GlycopeptideDockingProtocol::clone ( ) const

required in the context of the parser/scripting scheme

Reimplemented from protocols::moves::Mover.

◆ copy_data()

void protocols::glycopeptide_docking::GlycopeptideDockingProtocol::copy_data ( GlycopeptideDockingProtocol object_to_copy_to,
GlycopeptideDockingProtocol const &  object_to_copy_from 

Copy protocol data.

private methods ///

Copy private data, called by copy constructor

References constraint_setter_, flags_, mc_, ref_pose_, and sf_.

Referenced by GlycopeptideDockingProtocol(), and operator=().

◆ fresh_instance()

protocols::moves::MoverOP protocols::glycopeptide_docking::GlycopeptideDockingProtocol::fresh_instance ( ) const

required in the context of the parser/scripting scheme

Reimplemented from protocols::moves::Mover.

◆ get_name()

std::string protocols::glycopeptide_docking::GlycopeptideDockingProtocol::get_name ( ) const

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

Implements protocols::moves::Mover.

References mover_name().

◆ mover_name()

std::string protocols::glycopeptide_docking::GlycopeptideDockingProtocol::mover_name ( )

◆ operator=()

GlycopeptideDockingProtocol & protocols::glycopeptide_docking::GlycopeptideDockingProtocol::operator= ( GlycopeptideDockingProtocol const &  object_to_copy)

Assignment operator.

References copy_data().

◆ parse_my_tag()

void protocols::glycopeptide_docking::GlycopeptideDockingProtocol::parse_my_tag ( utility::tag::TagCOP  tag,
basic::datacache::DataMap data 

Rosetta Scripts Support ///.

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

Reimplemented from protocols::moves::Mover.

References flags_.

◆ prepare_score_function()

void protocols::glycopeptide_docking::GlycopeptideDockingProtocol::prepare_score_function ( )

Prepare scorefunction. Currently the scorefunction is fixed by design. Benchmarking has not been done with other scorefunctions.

Prepares the score function used by the refinement and abinitio protocols.

References core::scoring::atom_pair_constraint, core::scoring::fa_elec, core::scoring::fa_sol, core::scoring::get_score_function(), core::scoring::hbond_bb_sc, core::scoring::hbond_lr_bb, core::scoring::hbond_sc, core::scoring::hbond_sr_bb, sf_, and core::scoring::sugar_bb.

Referenced by GlycopeptideDockingProtocol().

◆ provide_xml_schema()

void protocols::glycopeptide_docking::GlycopeptideDockingProtocol::provide_xml_schema ( utility::tag::XMLSchemaDefinition &  xsd)

◆ set_ref_pose_from_filename()

void protocols::glycopeptide_docking::GlycopeptideDockingProtocol::set_ref_pose_from_filename ( std::string const &  filename)

Set reference pose (native) from file name.

References protocols::abinitio::filename(), core::import_pose::PDB_file, core::import_pose::pose_from_file(), and ref_pose_.

◆ show()

void protocols::glycopeptide_docking::GlycopeptideDockingProtocol::show ( std::ostream &  output = std::cout) const

Show mover information.

Show the contents of the Mover.

Reimplemented from protocols::moves::Mover.

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

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

Member Data Documentation

◆ constraint_setter_

protocols::constraint_movers::ConstraintSetMoverOP protocols::glycopeptide_docking::GlycopeptideDockingProtocol::constraint_setter_

◆ flags_

protocols::glycopeptide_docking::GlycopeptideDockingFlagsOP protocols::glycopeptide_docking::GlycopeptideDockingProtocol::flags_

◆ ft_docking_

core::kinematics::FoldTreeOP protocols::glycopeptide_docking::GlycopeptideDockingProtocol::ft_docking_ =nullptr

Referenced by apply().

◆ ft_substrate_

core::kinematics::FoldTreeOP protocols::glycopeptide_docking::GlycopeptideDockingProtocol::ft_substrate_ =nullptr

Referenced by apply().

◆ mc_

protocols::moves::MonteCarloOP protocols::glycopeptide_docking::GlycopeptideDockingProtocol::mc_

Referenced by copy_data().

◆ ref_pose_

core::pose::PoseOP protocols::glycopeptide_docking::GlycopeptideDockingProtocol::ref_pose_ =nullptr

◆ sf_

core::scoring::ScoreFunctionOP protocols::glycopeptide_docking::GlycopeptideDockingProtocol::sf_

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