GlycomutagenesisProtocol Class Reference

This protocol exhaustively mutates and glycosylates every possible position of a given protein. More...

Inheritance diagram for GlycomutagenesisProtocol:

Public Member Functions
	GlycomutagenesisProtocol ()
	Default constructor. More...
	GlycomutagenesisProtocol (GlycomutagenesisProtocol const &object_to_copy)
	Copy constructor. More...
GlycomutagenesisProtocol &	operator= (GlycomutagenesisProtocol const &object_to_copy)
virtual	~GlycomutagenesisProtocol ()
virtual void	show (std::ostream &output=std::cout) const
	Generate string representation of GlycomutagenesisProtocol for debugging purposes. More...
virtual std::string	get_name () const
	Return the name of the Mover. More...
virtual moves::MoverOP	clone () const
virtual moves::MoverOP	fresh_instance () const
virtual void	apply (core::pose::Pose &pose)
	Apply the corresponding protocol to <pose>. More...

Static Public Member Functions
static void	register_options ()
	Register options with the option system. More...

Private Member Functions
void	set_commandline_options ()
void	init ()
void	copy_data (GlycomutagenesisProtocol &object_to_copy_to, GlycomutagenesisProtocol const &object_to_copy_from)
void	disulfide_treatment (core::pose::Pose &pose, core::uint const seqpos, Size const n_residues_left_of_site, Size const n_residues_right_of_site)

Private Attributes
string const	species_name_ = "c_jejuni"
string const	enzyme_name_ = "PglB"
scoring::ScoreFunctionOP	sf_
scoring::ScoreFunctionOP	sf_sugar_only_
kinematics::MoveMapOP	mm_
Real const	kt_ = 0.8
Size	n_cycles_ = 100
simple_moves::MutateResidueOP	mutator_
enzymatic_movers::GlycosyltransferaseMoverOP	glycosyltransferase_
minimization_packing::MinMoverOP	minimizer_
minimization_packing::PackRotamersMoverOP	packer_
simple_moves::SmallMoverOP	small_mover_
protocols::moves::MonteCarloOP	mc_

Detailed Description

This protocol exhaustively mutates and glycosylates every possible position of a given protein.

Constructor & Destructor Documentation

GlycomutagenesisProtocol() [1/2]

GlycomutagenesisProtocol::GlycomutagenesisProtocol ( )

inline

Default constructor.

References basic::init().

GlycomutagenesisProtocol() [2/2]

GlycomutagenesisProtocol::GlycomutagenesisProtocol ( GlycomutagenesisProtocol const &  object_to_copy )

inline

Copy constructor.

~GlycomutagenesisProtocol()

virtual GlycomutagenesisProtocol::~GlycomutagenesisProtocol ( )

inlinevirtual

Member Function Documentation

apply()

virtual void GlycomutagenesisProtocol::apply ( core::pose::Pose &  pose )

inlinevirtual

Apply the corresponding protocol to <pose>.

On each apply, the Mover glycosylates the pose at the residue position corresponding to the current model as designated by the job distributor, using the consensus sequence from c. jejuni PglB. This is currently hard-coded into the protocol, which is not yet intended for public use.

References utility::io::oc::cout, cycle(), create_a3b_hbs::i, bin_torsions::job, beta_nonlocal::pose, and show().

Referenced by pyrosetta.bindings.scores.simple_metrics.SimpleMetricDataAccessorBase::__setitem__(), pyrosetta.bindings.scores.base.PoseCacheAccessorBase::_maybe_delete_keys_from_sm_data(), and pyrosetta.distributed.tasks.rosetta_scripts.BaseRosettaScriptsTask::execute().

clone()

virtual moves::MoverOP GlycomutagenesisProtocol::clone ( ) const

inlinevirtual

copy_data()

void GlycomutagenesisProtocol::copy_data ( GlycomutagenesisProtocol &  object_to_copy_to, GlycomutagenesisProtocol const &  object_to_copy_from  )

inlineprivate

References glycosyltransferase_, mc_, minimizer_, mm_, mutator_, packer_, sf_, sf_sugar_only_, and small_mover_.

disulfide_treatment()

void GlycomutagenesisProtocol::disulfide_treatment ( core::pose::Pose &  pose, core::uint const  seqpos, Size const  n_residues_left_of_site, Size const  n_residues_right_of_site  )

inlineprivate

References utility::io::oc::cout, create_a3b_hbs::i, and beta_nonlocal::pose.

fresh_instance()

virtual moves::MoverOP GlycomutagenesisProtocol::fresh_instance ( ) const

inlinevirtual

get_name()

virtual std::string GlycomutagenesisProtocol::get_name ( ) const

inlinevirtual

Return the name of the Mover.

init()

void GlycomutagenesisProtocol::init ( )

inlineprivate

References pyrosetta.distributed.io::get_score_function(), basic::options::OptionKeys::frags::scoring::scoring, vancomycin::task, and test.G200_Module_Region::tf.

operator=()

GlycomutagenesisProtocol& GlycomutagenesisProtocol::operator= ( GlycomutagenesisProtocol const &  object_to_copy )

inline

register_options()

static void GlycomutagenesisProtocol::register_options ( )

inlinestatic

Register options with the option system.

References register_options().

set_commandline_options()

void GlycomutagenesisProtocol::set_commandline_options ( )

inlineprivate

References basic::options::OptionKeys::run::n_cycles, and option.

show()

virtual void GlycomutagenesisProtocol::show ( std::ostream &  output = std::cout ) const

inlinevirtual

Generate string representation of GlycomutagenesisProtocol for debugging purposes.

References bin_torsions::output, and show().

Referenced by pyrosetta.distributed.viewer.core.Viewer::__call__().

Member Data Documentation

enzyme_name_

string const GlycomutagenesisProtocol::enzyme_name_ = "PglB"

private

glycosyltransferase_

enzymatic_movers::GlycosyltransferaseMoverOP GlycomutagenesisProtocol::glycosyltransferase_

private

Referenced by copy_data().

kt_

Real const GlycomutagenesisProtocol::kt_ = 0.8

private

mc_

protocols::moves::MonteCarloOP GlycomutagenesisProtocol::mc_

private

Referenced by copy_data().

minimizer_

minimization_packing::MinMoverOP GlycomutagenesisProtocol::minimizer_

private

Referenced by copy_data().

mm_

kinematics::MoveMapOP GlycomutagenesisProtocol::mm_

private

Referenced by copy_data().

mutator_

simple_moves::MutateResidueOP GlycomutagenesisProtocol::mutator_

private

Referenced by copy_data().

n_cycles_

Size GlycomutagenesisProtocol::n_cycles_ = 100

private

packer_

minimization_packing::PackRotamersMoverOP GlycomutagenesisProtocol::packer_

private

Referenced by copy_data().

sf_

scoring::ScoreFunctionOP GlycomutagenesisProtocol::sf_

private

Referenced by copy_data().

sf_sugar_only_

scoring::ScoreFunctionOP GlycomutagenesisProtocol::sf_sugar_only_

private

Referenced by copy_data().

small_mover_

simple_moves::SmallMoverOP GlycomutagenesisProtocol::small_mover_

private

Referenced by copy_data().

species_name_

string const GlycomutagenesisProtocol::species_name_ = "c_jejuni"

private

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

• src/apps/pilot/labonte/glycomutagenesis.cc