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protocols::glycopeptide_docking::GlycopeptideDockingLowResRefinement Class Reference

Low resolution refinement of substrate. More...

#include <GlycopeptideDockingLowResRefinement.hh>

Inheritance diagram for protocols::glycopeptide_docking::GlycopeptideDockingLowResRefinement:
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Public Member Functions

 GlycopeptideDockingLowResRefinement ()
 Constructors ///. More...
 
 GlycopeptideDockingLowResRefinement (protocols::glycopeptide_docking::GlycopeptideDockingFlagsOP flags, core::scoring::ScoreFunctionOP sf, core::kinematics::FoldTreeOP ft_docking, core::kinematics::FoldTreeOP ft_substrate)
 Constructor requiring flags, scorefunction sf and folding trees. More...
 
 GlycopeptideDockingLowResRefinement (protocols::glycopeptide_docking::GlycopeptideDockingFlagsOP flags, core::scoring::ScoreFunctionOP sf)
 Constructor that only requires the GlycopeptideDockingFlagsOP flags and scorefunction sf. More...
 
 GlycopeptideDockingLowResRefinement (GlycopeptideDockingLowResRefinement const &src)
 Copy constructor (not needed unless you need deep copies) More...
 
 ~GlycopeptideDockingLowResRefinement () 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 the contents of the Mover. 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...
 
void set_options (protocols::glycopeptide_docking::GlycopeptideDockingFlagsOP flags)
 Getters and setters for sf, foldtrees, flags. More...
 
protocols::glycopeptide_docking::GlycopeptideDockingFlagsOP get_options ()
 
void set_scorefunction (core::scoring::ScoreFunctionOP sf)
 
core::scoring::ScoreFunctionOP get_scorefunction ()
 
void set_docking_foldtree (core::kinematics::FoldTreeOP ft_docking)
 
core::kinematics::FoldTreeCOP get_docking_foldtree ()
 
void set_substrate_foldtree (core::kinematics::FoldTreeOP ft_substrate)
 
core::kinematics::FoldTreeCOP get_substrate_foldtree ()
 
- 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
 
virtual void parse_my_tag (TagCOP tag, basic::datacache::DataMap &data)
 Called by MoverFactory when constructing new Movers. Takes care of the specific mover's parsing. More...
 
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 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 setup_backbone_and_jump_movemap ()
 
void sample_torsions (core::pose::Pose &pose, core::Size cycles, core::Real &acceptance_rate, core::kinematics::MoveMapOP mm)
 private methods /// More...
 

Private Attributes

protocols::glycopeptide_docking::GlycopeptideDockingFlagsOP flags_
 Flags object with options specifying glycopeptide_docking options. More...
 
core::scoring::ScoreFunctionOP sf_
 Scorefunction. More...
 
core::kinematics::FoldTreeOP ft_docking_ =nullptr
 Foldtree for peptide-enzyme docking. More...
 
core::kinematics::FoldTreeOP ft_substrate_ =nullptr
 Foldtree for sampling peptide degrees of freedon. More...
 
protocols::moves::MonteCarloOP mc_
 Monte Carlo object for sampling. More...
 
protocols::minimization_packing::MinMoverOP torsion_minimizer_
 Min mover for minimizing torsional dofs. More...
 
protocols::minimization_packing::MinMoverOP jump_minimizer_
 Min mover for minmizing peptide-enzyme jump. More...
 

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

Low resolution refinement of substrate.

Low resolution refinement primarly for sampling peptide conformational space. We use simulated annealing varying mc temperature from 2.0 to 0.6 (final) temperature. The protocol applies the following steps over 30 cycles of simulated annealing:

  1. rigidbody perturber mover
  2. minimization across the jump
  3. Samples torsions of the peptide with small and shear mover
  4. Minimizes peptide

Constructor & Destructor Documentation

protocols::glycopeptide_docking::GlycopeptideDockingLowResRefinement::GlycopeptideDockingLowResRefinement ( )

Constructors ///.

Default constructor

protocols::glycopeptide_docking::GlycopeptideDockingLowResRefinement::GlycopeptideDockingLowResRefinement ( protocols::glycopeptide_docking::GlycopeptideDockingFlagsOP  flags,
core::scoring::ScoreFunctionOP  sf,
core::kinematics::FoldTreeOP  ft_docking,
core::kinematics::FoldTreeOP  ft_substrate 
)

Constructor requiring flags, scorefunction sf and folding trees.

Sets up movemap for torsion sampling. Sets jumps. Torsions are sampled for backbone and chi angle for the peptide substrate only (along with glycans that branch out). Sets up minimizers for peptide torsion sampling and for enzyme-peptide interface jump.

Constructor initialized with the GlycopeptideDockingFlagsOP flags
(all options for setting up glycopeptide_docking), scorefunction sf and fold trees for peptide-enzyme docking and sampling the substrate. Currently, the use of ft_substrate is disabled as it worsened predictions.

References setup_backbone_and_jump_movemap().

protocols::glycopeptide_docking::GlycopeptideDockingLowResRefinement::GlycopeptideDockingLowResRefinement ( protocols::glycopeptide_docking::GlycopeptideDockingFlagsOP  flags,
core::scoring::ScoreFunctionOP  sf 
)

Constructor that only requires the GlycopeptideDockingFlagsOP flags and scorefunction sf.

The foldtree is automatically setup with a util function based on options
in the flags.

References setup_backbone_and_jump_movemap().

protocols::glycopeptide_docking::GlycopeptideDockingLowResRefinement::GlycopeptideDockingLowResRefinement ( GlycopeptideDockingLowResRefinement const &  src)

Copy constructor (not needed unless you need deep copies)

Copy constructor.

protocols::glycopeptide_docking::GlycopeptideDockingLowResRefinement::~GlycopeptideDockingLowResRefinement ( )
override

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

Member Function Documentation

void protocols::glycopeptide_docking::GlycopeptideDockingLowResRefinement::apply ( core::pose::Pose pose)
overridevirtual

Mover Methods ///.

Apply the mover

Low resolution refinement primarly for sampling peptide conformational space. We use simulated annealing varying mc temperature from 2.0 to 0.6 (final) temperature. The protocol applies the following steps over 30 cycles of simulated annealing:

  1. rigidbody perturber mover
  2. minimization across the jump
  3. Samples torsions of the peptide with small and shear mover
  4. Minimizes peptide

Implements protocols::moves::Mover.

References protocols::glycopeptide_docking::calculate_sampled_distance(), flags_, core::pose::Pose::fold_tree(), ft_docking_, protocols::jd2::JobDistributor::get_instance(), jump_minimizer_, mc_, sample_torsions(), protocols::glycopeptide_docking::setup_glycosylation_foldtree(), sf_, torsion_minimizer_, protocols::TR(), and protocols::glycopeptide_docking::write_debug_pdb().

Referenced by protocols::glycopeptide_docking::GlycopeptideDockingProtocol::apply().

protocols::moves::MoverOP protocols::glycopeptide_docking::GlycopeptideDockingLowResRefinement::clone ( ) const
overridevirtual

required in the context of the parser/scripting scheme

Reimplemented from protocols::moves::Mover.

protocols::moves::MoverOP protocols::glycopeptide_docking::GlycopeptideDockingLowResRefinement::fresh_instance ( ) const
overridevirtual

required in the context of the parser/scripting scheme

Reimplemented from protocols::moves::Mover.

core::kinematics::FoldTreeCOP protocols::glycopeptide_docking::GlycopeptideDockingLowResRefinement::get_docking_foldtree ( )
inline

References ft_docking_.

std::string protocols::glycopeptide_docking::GlycopeptideDockingLowResRefinement::get_name ( ) const
overridevirtual

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

Implements protocols::moves::Mover.

References mover_name().

protocols::glycopeptide_docking::GlycopeptideDockingFlagsOP protocols::glycopeptide_docking::GlycopeptideDockingLowResRefinement::get_options ( )
inline

References flags_.

core::scoring::ScoreFunctionOP protocols::glycopeptide_docking::GlycopeptideDockingLowResRefinement::get_scorefunction ( )
inline

References sf_.

core::kinematics::FoldTreeCOP protocols::glycopeptide_docking::GlycopeptideDockingLowResRefinement::get_substrate_foldtree ( )
inline

References ft_substrate_.

std::string protocols::glycopeptide_docking::GlycopeptideDockingLowResRefinement::mover_name ( )
static

Referenced by get_name().

void protocols::glycopeptide_docking::GlycopeptideDockingLowResRefinement::sample_torsions ( core::pose::Pose pose,
core::Size  cycles,
core::Real acceptance_rate,
core::kinematics::MoveMapOP  mm 
)
private

private methods ///

Samples torsional degrees of freedom with small and shear mover.

References protocols::moves::accept_reject, and mc_.

Referenced by apply().

void protocols::glycopeptide_docking::GlycopeptideDockingLowResRefinement::set_docking_foldtree ( core::kinematics::FoldTreeOP  ft_docking)
inline

References ft_docking_.

void protocols::glycopeptide_docking::GlycopeptideDockingLowResRefinement::set_options ( protocols::glycopeptide_docking::GlycopeptideDockingFlagsOP  flags)
inline

Getters and setters for sf, foldtrees, flags.

References flags_.

void protocols::glycopeptide_docking::GlycopeptideDockingLowResRefinement::set_scorefunction ( core::scoring::ScoreFunctionOP  sf)
inline

References sf_.

void protocols::glycopeptide_docking::GlycopeptideDockingLowResRefinement::set_substrate_foldtree ( core::kinematics::FoldTreeOP  ft_substrate)
inline

References ft_substrate_.

void protocols::glycopeptide_docking::GlycopeptideDockingLowResRefinement::setup_backbone_and_jump_movemap ( )
private
void protocols::glycopeptide_docking::GlycopeptideDockingLowResRefinement::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::glycopeptide_docking::operator<<().

Member Data Documentation

protocols::glycopeptide_docking::GlycopeptideDockingFlagsOP protocols::glycopeptide_docking::GlycopeptideDockingLowResRefinement::flags_
private

Flags object with options specifying glycopeptide_docking options.

Referenced by apply(), get_options(), set_options(), and setup_backbone_and_jump_movemap().

core::kinematics::FoldTreeOP protocols::glycopeptide_docking::GlycopeptideDockingLowResRefinement::ft_docking_ =nullptr
private

Foldtree for peptide-enzyme docking.

Referenced by apply(), get_docking_foldtree(), and set_docking_foldtree().

core::kinematics::FoldTreeOP protocols::glycopeptide_docking::GlycopeptideDockingLowResRefinement::ft_substrate_ =nullptr
private

Foldtree for sampling peptide degrees of freedon.

Referenced by get_substrate_foldtree(), and set_substrate_foldtree().

protocols::minimization_packing::MinMoverOP protocols::glycopeptide_docking::GlycopeptideDockingLowResRefinement::jump_minimizer_
private

Min mover for minmizing peptide-enzyme jump.

Referenced by apply(), and setup_backbone_and_jump_movemap().

protocols::moves::MonteCarloOP protocols::glycopeptide_docking::GlycopeptideDockingLowResRefinement::mc_
private

Monte Carlo object for sampling.

Referenced by apply(), and sample_torsions().

core::scoring::ScoreFunctionOP protocols::glycopeptide_docking::GlycopeptideDockingLowResRefinement::sf_
private
protocols::minimization_packing::MinMoverOP protocols::glycopeptide_docking::GlycopeptideDockingLowResRefinement::torsion_minimizer_
private

Min mover for minimizing torsional dofs.

Referenced by apply(), and setup_backbone_and_jump_movemap().


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