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DockGlycansProtocol Class Reference

The protocol ported from dock_glycans.py. More...

Inheritance diagram for DockGlycansProtocol:
Inheritance graph
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Public Member Functions

 DockGlycansProtocol ()
 Default constructor. More...
 
 DockGlycansProtocol (DockGlycansProtocol const &object_to_copy)
 Copy constructor. More...
 
DockGlycansProtocol & operator= (DockGlycansProtocol const &object_to_copy)
 
 ~DockGlycansProtocol () override=default
 
void show (std::ostream &output=std::cout) const override
 Generate string representation of DockGlycansProtocol for debugging purposes. More...
 
std::string get_name () const override
 Return the name of the Mover. More...
 
moves::MoverOP clone () const override
 
moves::MoverOP fresh_instance () const override
 
void apply (core::pose::Pose &pose) override
 Apply the corresponding protocol to <pose>. More...
 
void score_function (core::scoring::ScoreFunctionOP input_sf)
 
void set_ref_pose_from_filename (std::string const &filename)
 

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 (DockGlycansProtocol &object_to_copy_to, DockGlycansProtocol const &object_to_copy_from)
 
void determine_docking_partners (core::pose::Pose const &pose)
 
void prepare_scoring_function ()
 
void ramp_score_weight (core::scoring::ScoreType const method, core::Real const target, core::Real const fraction_completion)
 
void record_pose_metrics (core::pose::Pose const &pose, protocols::jd2::Job &job, utility::vector1< int > const jumps)
 

Private Attributes

std::string upstream_chains_
 
std::string downstream_chains_
 
core::uint first_ligand_residue_
 
core::scoring::ScoreFunctionOP sf_
 
core::pose::PoseOP ref_pose_
 
core::Real Hbond_mult_
 
core::Real elec_mult_
 
core::Real sol_mult_
 
core::Real atr_mult_
 
core::Real rep_mult_
 
core::Real target_atr_
 
core::Real target_rep_
 
core::Angle rot_
 
core::Distance trans_
 
bool idealize_rings_
 
bool lock_rings_
 
core::kinematics::MoveMapOP jump_mm_
 
core::kinematics::MoveMapOP ring_mm_
 
core::kinematics::MoveMapOP torsion_mm_
 
protocols::constraint_movers::ConstraintSetMoverOP constraint_setter_
 
protocols::rigid::RigidBodyRandomizeMoverOP randomizerA_
 
protocols::docking::FaDockingSlideIntoContactOP slider_
 
protocols::rigid::RigidBodyPerturbMoverOP perturber_
 
protocols::minimization_packing::MinMoverOP jump_minimizer_
 
protocols::simple_moves::RingConformationMoverOP ring_mover_
 
protocols::simple_moves::SmallMoverOP small_mover_
 
protocols::simple_moves::ShearMoverOP shear_mover_
 
protocols::minimization_packing::PackRotamersMoverOP packer_
 
protocols::minimization_packing::MinMoverOP torsion_minimizer_
 
core::Size n_cycles_
 
core::Real kt_
 
protocols::moves::MonteCarloOP mc_
 

Static Private Attributes

static core::uint const JUMP_NUM
 
static core::Real const STARTING_RAMP_DOWN_FACTOR
 
static core::Real const STARTING_RAMP_UP_FACTOR
 

Detailed Description

The protocol ported from dock_glycans.py.

Constructor & Destructor Documentation

DockGlycansProtocol::DockGlycansProtocol ( )
inline

Default constructor.

References basic::init().

DockGlycansProtocol::DockGlycansProtocol ( DockGlycansProtocol const &  object_to_copy)
inline

Copy constructor.

DockGlycansProtocol::~DockGlycansProtocol ( )
overridedefault

Member Function Documentation

void DockGlycansProtocol::apply ( core::pose::Pose &  pose)
inlineoverride

Apply the corresponding protocol to <pose>.

References utility::io::oc::cout, basic::options::OptionKeys::docking::docking, basic::options::OptionKeys::docking::partners, demo.D010_Pose_structure::pose, basic::options::OptionKeys::hotspot::residue, numeric::random::rg(), basic::options::OptionKeys::rigid::rigid, basic::options::OptionKeys::frags::scoring::scoring, show(), test.G200_Module_Region::task, and numeric::random::uniform().

Referenced by pyrosetta.distributed.tasks.rosetta_scripts.BaseRosettaScriptsTask::execute().

moves::MoverOP DockGlycansProtocol::clone ( ) const
inlineoverride
void DockGlycansProtocol::copy_data ( DockGlycansProtocol &  object_to_copy_to,
DockGlycansProtocol const &  object_to_copy_from 
)
inlineprivate

References atr_mult_, constraint_setter_, downstream_chains_, elec_mult_, first_ligand_residue_, Hbond_mult_, idealize_rings_, jump_minimizer_, jump_mm_, kt_, lock_rings_, mc_, n_cycles_, packer_, perturber_, randomizerA_, ref_pose_, rep_mult_, ring_mm_, ring_mover_, rot_, sf_, shear_mover_, slider_, small_mover_, sol_mult_, target_atr_, target_rep_, torsion_minimizer_, torsion_mm_, trans_, and upstream_chains_.

void DockGlycansProtocol::determine_docking_partners ( core::pose::Pose const &  pose)
inlineprivate
moves::MoverOP DockGlycansProtocol::fresh_instance ( ) const
inlineoverride
std::string DockGlycansProtocol::get_name ( ) const
inlineoverride

Return the name of the Mover.

References DRRAFTER::type.

void DockGlycansProtocol::init ( )
inlineprivate

References options, test.G200_Module_Region::task, test.G200_Module_Region::tf, and DRRAFTER::type.

DockGlycansProtocol& DockGlycansProtocol::operator= ( DockGlycansProtocol const &  object_to_copy)
inline
void DockGlycansProtocol::prepare_scoring_function ( )
inlineprivate

References basic::options::OptionKeys::frags::scoring::scoring.

void DockGlycansProtocol::ramp_score_weight ( core::scoring::ScoreType const  method,
core::Real const  target,
core::Real const  fraction_completion 
)
inlineprivate
void DockGlycansProtocol::record_pose_metrics ( core::pose::Pose const &  pose,
protocols::jd2::Job &  job,
utility::vector1< int > const  jumps 
)
inlineprivate

References utility::io::oc::cout, basic::options::OptionKeys::docking::docking, ligand_rmsd(), and basic::options::OptionKeys::frags::scoring::scoring.

static void DockGlycansProtocol::register_options ( )
inlinestatic

Register options with the option system.

References basic::options::OptionKeys::constraints::cst_fa_file, basic::options::OptionKeys::rings::idealize_rings, basic::options::OptionKeys::rings::lock_rings, basic::options::OptionKeys::run::n_cycles, option, options, and register_options().

void DockGlycansProtocol::score_function ( core::scoring::ScoreFunctionOP  input_sf)
inline

Referenced by pyrosetta.distributed.tasks.score.ScorePoseTask::execute().

void DockGlycansProtocol::set_commandline_options ( )
inlineprivate

References basic::options::OptionKeys::constraints::cst_fa_file, basic::options::OptionKeys::rings::idealize_rings, basic::options::OptionKeys::rings::lock_rings, basic::options::OptionKeys::run::n_cycles, option, and options.

void DockGlycansProtocol::set_ref_pose_from_filename ( std::string const &  filename)
inline

References pyrosetta.distributed.io::pose_from_file.

void DockGlycansProtocol::show ( std::ostream &  output = std::cout) const
inlineoverride

Generate string representation of DockGlycansProtocol for debugging purposes.

References basic::options::OptionKeys::cp::output, and show().

Member Data Documentation

core::Real DockGlycansProtocol::atr_mult_
private

Referenced by copy_data().

protocols::constraint_movers::ConstraintSetMoverOP DockGlycansProtocol::constraint_setter_
private

Referenced by copy_data().

std::string DockGlycansProtocol::downstream_chains_
private

Referenced by copy_data().

core::Real DockGlycansProtocol::elec_mult_
private

Referenced by copy_data().

core::uint DockGlycansProtocol::first_ligand_residue_
private

Referenced by copy_data().

core::Real DockGlycansProtocol::Hbond_mult_
private

Referenced by copy_data().

bool DockGlycansProtocol::idealize_rings_
private

Referenced by copy_data().

protocols::minimization_packing::MinMoverOP DockGlycansProtocol::jump_minimizer_
private

Referenced by copy_data().

core::kinematics::MoveMapOP DockGlycansProtocol::jump_mm_
private

Referenced by copy_data().

core::uint const DockGlycansProtocol::JUMP_NUM
staticprivate
core::Real DockGlycansProtocol::kt_
private

Referenced by copy_data().

bool DockGlycansProtocol::lock_rings_
private

Referenced by copy_data().

protocols::moves::MonteCarloOP DockGlycansProtocol::mc_
private

Referenced by copy_data().

core::Size DockGlycansProtocol::n_cycles_
private

Referenced by copy_data().

protocols::minimization_packing::PackRotamersMoverOP DockGlycansProtocol::packer_
private

Referenced by copy_data().

protocols::rigid::RigidBodyPerturbMoverOP DockGlycansProtocol::perturber_
private

Referenced by copy_data().

protocols::rigid::RigidBodyRandomizeMoverOP DockGlycansProtocol::randomizerA_
private

Referenced by copy_data().

core::pose::PoseOP DockGlycansProtocol::ref_pose_
private

Referenced by copy_data().

core::Real DockGlycansProtocol::rep_mult_
private

Referenced by copy_data().

core::kinematics::MoveMapOP DockGlycansProtocol::ring_mm_
private

Referenced by copy_data().

protocols::simple_moves::RingConformationMoverOP DockGlycansProtocol::ring_mover_
private

Referenced by copy_data().

core::Angle DockGlycansProtocol::rot_
private

Referenced by copy_data().

core::scoring::ScoreFunctionOP DockGlycansProtocol::sf_
private

Referenced by copy_data().

protocols::simple_moves::ShearMoverOP DockGlycansProtocol::shear_mover_
private

Referenced by copy_data().

protocols::docking::FaDockingSlideIntoContactOP DockGlycansProtocol::slider_
private

Referenced by copy_data().

protocols::simple_moves::SmallMoverOP DockGlycansProtocol::small_mover_
private

Referenced by copy_data().

core::Real DockGlycansProtocol::sol_mult_
private

Referenced by copy_data().

core::Real const DockGlycansProtocol::STARTING_RAMP_DOWN_FACTOR
staticprivate
core::Real const DockGlycansProtocol::STARTING_RAMP_UP_FACTOR
staticprivate
core::Real DockGlycansProtocol::target_atr_
private

Referenced by copy_data().

core::Real DockGlycansProtocol::target_rep_
private

Referenced by copy_data().

protocols::minimization_packing::MinMoverOP DockGlycansProtocol::torsion_minimizer_
private

Referenced by copy_data().

core::kinematics::MoveMapOP DockGlycansProtocol::torsion_mm_
private

Referenced by copy_data().

core::Distance DockGlycansProtocol::trans_
private

Referenced by copy_data().

std::string DockGlycansProtocol::upstream_chains_
private

Referenced by copy_data().

The documentation for this class was generated from the following file:
Generated on Thu Mar 28 2019 04:49:52 for Rosetta by   doxygen 1.8.7