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protocols::glycopeptide_docking::GlycopeptideDockingHighResRefinement Class Reference

High resolution refinement of glycosyltransferase substrate. More...

#include <GlycopeptideDockingHighResRefinement.hh>

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

 GlycopeptideDockingHighResRefinement ()
 Constructors ///. More...
 
 GlycopeptideDockingHighResRefinement (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...
 
 GlycopeptideDockingHighResRefinement (protocols::glycopeptide_docking::GlycopeptideDockingFlagsOP flags, core::scoring::ScoreFunctionOP sf)
 Constructor that only requires the GlycopeptideDockingFlagsOP flags and scorefunction sf. More...
 
 GlycopeptideDockingHighResRefinement (GlycopeptideDockingHighResRefinement const &src)
 Copy constructor (not needed unless you need deep copies) More...
 
 ~GlycopeptideDockingHighResRefinement () override
 Destructor (important for properly forward-declaring smart-pointer members) More...
 
void setup ()
 Mover Methods ///. More...
 
void apply (core::pose::Pose &pose) override
 Apply the mover. More...
 
void show (std::ostream &output=std::cout) const override
 show mover details 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
 get 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 ()
 
void set_target_attractive_weight (core::Real w)
 
core::Real get_target_attractive_weight ()
 
void set_target_repulsive_weight (core::Real w)
 
core::Real get_target_repulsive_weight ()
 
- 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 ()
 get mover name More...
 
- 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 ramp_score_weight (core::scoring::ScoreType const method, core::Real const target, core::Real const fraction_completion)
 Ramps up weight for repulsive term and ramps down attractive LJ term. More...
 

Private Attributes

protocols::glycopeptide_docking::GlycopeptideDockingFlagsOP flags_
 
core::Real kt_
 Boltmann sampling temperature. More...
 
core::Real target_atr_
 Final weight of the attractive force term. More...
 
core::Real target_rep_
 Final weight of the repulsive force term. More...
 
core::Real starting_ramp_down_factor_
 Fractional factor by which the attractive weight is ramped down. More...
 
core::Real starting_ramp_up_factor_
 Fractional factor by which the repulsive weight is ramped up. More...
 
core::scoring::ScoreFunctionOP sf_
 
core::kinematics::FoldTreeOP ft_docking_
 
core::kinematics::FoldTreeOP ft_substrate_
 
protocols::moves::MonteCarloOP mc_
 
protocols::rigid::RigidBodyPerturbMoverOP perturber_
 
protocols::minimization_packing::MinMoverOP jump_minimizer_
 
protocols::minimization_packing::MinMoverOP torsion_minimizer_
 
protocols::simple_moves::SmallMoverOP small_mover_
 
protocols::simple_moves::ShearMoverOP shear_mover_
 
protocols::minimization_packing::PackRotamersMoverOP packer_substrate_
 
protocols::minimization_packing::PackRotamersMoverOP packer_interface_
 

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

High resolution refinement of glycosyltransferase substrate.

Applies a set of samplers to the pose in high resolution mode. At the beginning, the fa_atr term is upweighted and the fa_rep term is downweighted. The terms are ramped down and up respectively to their score function weights over n_cycles_. For each cycles, the pose is subjected to:

  1. N cycles of rigid body moves 1.1. Rigid body perturbation 1.2 Sidechain packing of substrate 1.3 Sidechain packing of interface 1.4 Minimization across the substrate-enzyme jump 1.5 Metropolis criterion (MCM with 1.4)
  2. N cycles of torsion moves "induced fit" 2.1 Apply small or shear mover 2.2 Sidechain packing of substrate 2.3 Sidechain packing of interface 2.4 Minimize and apply Metropolis criterion (MCM)

Constructor & Destructor Documentation

protocols::glycopeptide_docking::GlycopeptideDockingHighResRefinement::GlycopeptideDockingHighResRefinement ( )

Constructors ///.

Default constructor

Default constructors does not setup anything. Various getters and setters are provided to setup all options.

Default constructor

protocols::glycopeptide_docking::GlycopeptideDockingHighResRefinement::GlycopeptideDockingHighResRefinement ( 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.

Constructor with arguments.

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().

protocols::glycopeptide_docking::GlycopeptideDockingHighResRefinement::GlycopeptideDockingHighResRefinement ( 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().

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

Copy constructor (not needed unless you need deep copies)

Copy constructor.

protocols::glycopeptide_docking::GlycopeptideDockingHighResRefinement::~GlycopeptideDockingHighResRefinement ( )
override

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

Member Function Documentation

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

Apply the mover.

Applies a set of samplers to the pose in high resolution mode. At the beginning, the fa_atr term is upweighted and the fa_rep term is downweighted. The terms are ramped down and up respectively to their score function weights over n_cycles_. For each cycles, the pose is subjected to:

  1. N cycles of rigid body moves 1.1. Rigid body perturbation 1.2 Sidechain packing of substrate 1.3 Sidechain packing of interface 1.4 Minimization across the substrate-enzyme jump 1.5 Metropolis criterion (MCM with 1.4)
  2. N cycles of torsion moves "induced fit" 2.1 Apply small or shear mover 2.2 Sidechain packing of substrate 2.3 Sidechain packing of interface 2.4 Minimize and apply Metropolis criterion (MCM) TODO: add sugar bbsampler to sample torsions for higher glycans. Protocol currently tested for monosaccharides. TODO: Test sampling of "donor residue" in the torsional space.

Implements protocols::moves::Mover.

References protocols::glycopeptide_docking::calculate_sampled_distance(), core::scoring::fa_atr, core::scoring::fa_rep, flags_, core::pose::Pose::fold_tree(), ft_docking_, protocols::jd2::JobDistributor::get_instance(), jump_minimizer_, kt_, mc_, packer_interface_, packer_substrate_, perturber_, ramp_score_weight(), protocols::glycopeptide_docking::setup_glycosylation_foldtree(), sf_, shear_mover_, show(), small_mover_, starting_ramp_down_factor_, starting_ramp_up_factor_, target_atr_, target_rep_, torsion_minimizer_, protocols::TR(), and protocols::glycopeptide_docking::write_debug_pdb().

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

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

required in the context of the parser/scripting scheme

Reimplemented from protocols::moves::Mover.

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

required in the context of the parser/scripting scheme

Reimplemented from protocols::moves::Mover.

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

References ft_docking_.

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

get name

Implements protocols::moves::Mover.

References mover_name().

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

References flags_.

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

References sf_.

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

References ft_substrate_.

core::Real protocols::glycopeptide_docking::GlycopeptideDockingHighResRefinement::get_target_attractive_weight ( )
inline

References target_atr_.

core::Real protocols::glycopeptide_docking::GlycopeptideDockingHighResRefinement::get_target_repulsive_weight ( )
inline

References target_rep_.

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

get mover name

Referenced by get_name().

void protocols::glycopeptide_docking::GlycopeptideDockingHighResRefinement::ramp_score_weight ( core::scoring::ScoreType const  method,
core::Real const  target,
core::Real const  fraction_completion 
)
private

Ramps up weight for repulsive term and ramps down attractive LJ term.

Function to ramp up and ramp down score weights. fa_atr is ramped down from an upweighted weight. fa_rep is ramped up from an downweighted weight. The refinement protocol currently uses it to ramp down attractive terms and ramp up repulsive terms.

References sf_, starting_ramp_down_factor_, and starting_ramp_up_factor_.

Referenced by apply().

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

References ft_docking_.

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

Getters and setters for sf, foldtrees, flags.

References flags_.

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

References sf_.

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

References ft_substrate_.

void protocols::glycopeptide_docking::GlycopeptideDockingHighResRefinement::set_target_attractive_weight ( core::Real  w)
inline

References target_atr_.

void protocols::glycopeptide_docking::GlycopeptideDockingHighResRefinement::set_target_repulsive_weight ( core::Real  w)
inline

References target_rep_.

void protocols::glycopeptide_docking::GlycopeptideDockingHighResRefinement::setup ( )
void protocols::glycopeptide_docking::GlycopeptideDockingHighResRefinement::show ( std::ostream &  output = std::cout) const
overridevirtual

Member Data Documentation

protocols::glycopeptide_docking::GlycopeptideDockingFlagsOP protocols::glycopeptide_docking::GlycopeptideDockingHighResRefinement::flags_
private

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

core::kinematics::FoldTreeOP protocols::glycopeptide_docking::GlycopeptideDockingHighResRefinement::ft_docking_
private
core::kinematics::FoldTreeOP protocols::glycopeptide_docking::GlycopeptideDockingHighResRefinement::ft_substrate_
private
protocols::minimization_packing::MinMoverOP protocols::glycopeptide_docking::GlycopeptideDockingHighResRefinement::jump_minimizer_
private

Referenced by apply(), and setup().

core::Real protocols::glycopeptide_docking::GlycopeptideDockingHighResRefinement::kt_
private

Boltmann sampling temperature.

Referenced by apply(), and setup().

protocols::moves::MonteCarloOP protocols::glycopeptide_docking::GlycopeptideDockingHighResRefinement::mc_
private

Referenced by apply().

protocols::minimization_packing::PackRotamersMoverOP protocols::glycopeptide_docking::GlycopeptideDockingHighResRefinement::packer_interface_
private

Referenced by apply(), and setup().

protocols::minimization_packing::PackRotamersMoverOP protocols::glycopeptide_docking::GlycopeptideDockingHighResRefinement::packer_substrate_
private

Referenced by apply(), and setup().

protocols::rigid::RigidBodyPerturbMoverOP protocols::glycopeptide_docking::GlycopeptideDockingHighResRefinement::perturber_
private

Referenced by apply(), and setup().

core::scoring::ScoreFunctionOP protocols::glycopeptide_docking::GlycopeptideDockingHighResRefinement::sf_
private
protocols::simple_moves::ShearMoverOP protocols::glycopeptide_docking::GlycopeptideDockingHighResRefinement::shear_mover_
private

Referenced by apply(), and setup().

protocols::simple_moves::SmallMoverOP protocols::glycopeptide_docking::GlycopeptideDockingHighResRefinement::small_mover_
private

Referenced by apply(), and setup().

core::Real protocols::glycopeptide_docking::GlycopeptideDockingHighResRefinement::starting_ramp_down_factor_
private

Fractional factor by which the attractive weight is ramped down.

Referenced by apply(), ramp_score_weight(), and setup().

core::Real protocols::glycopeptide_docking::GlycopeptideDockingHighResRefinement::starting_ramp_up_factor_
private

Fractional factor by which the repulsive weight is ramped up.

Referenced by apply(), ramp_score_weight(), and setup().

core::Real protocols::glycopeptide_docking::GlycopeptideDockingHighResRefinement::target_atr_
private

Final weight of the attractive force term.

Set to be the same as ref2015 weight

Referenced by apply(), get_target_attractive_weight(), set_target_attractive_weight(), and setup().

core::Real protocols::glycopeptide_docking::GlycopeptideDockingHighResRefinement::target_rep_
private

Final weight of the repulsive force term.

Set to be the same as ref2015 weight

Referenced by apply(), get_target_repulsive_weight(), set_target_repulsive_weight(), and setup().

protocols::minimization_packing::MinMoverOP protocols::glycopeptide_docking::GlycopeptideDockingHighResRefinement::torsion_minimizer_
private

Referenced by apply(), and setup().


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