DockGlycansProtocol Class Reference

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

Inheritance diagram for DockGlycansProtocol:

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() [1/2]

DockGlycansProtocol::DockGlycansProtocol ( )

inline

Default constructor.

References basic::init().

DockGlycansProtocol() [2/2]

DockGlycansProtocol::DockGlycansProtocol ( DockGlycansProtocol const &  object_to_copy )

inline

Copy constructor.

~DockGlycansProtocol()

DockGlycansProtocol::~DockGlycansProtocol ( )

overridedefault

Member Function Documentation

apply()

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

inlineoverride

Apply the corresponding protocol to <pose>.

References utility::io::oc::cout, cycle(), BundlePairRmsdCalculator::fraction, bin_torsions::job, basic::options::OptionKeys::docking::partners, beta_nonlocal::pose, residue, numeric::random::rg(), basic::options::OptionKeys::frags::scoring::scoring, show(), vancomycin::task, and numeric::random::uniform().

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

clone()

moves::MoverOP DockGlycansProtocol::clone ( ) const

inlineoverride

copy_data()

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_.

determine_docking_partners()

void DockGlycansProtocol::determine_docking_partners ( core::pose::Pose const &  pose )

inlineprivate

References create_a3b_hbs::pdb_info, and beta_nonlocal::pose.

fresh_instance()

moves::MoverOP DockGlycansProtocol::fresh_instance ( ) const

inlineoverride

get_name()

std::string DockGlycansProtocol::get_name ( ) const

inlineoverride

Return the name of the Mover.

init()

void DockGlycansProtocol::init ( )

inlineprivate

References vancomycin::task, and test.G200_Module_Region::tf.

operator=()

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

inline

prepare_scoring_function()

void DockGlycansProtocol::prepare_scoring_function ( )

inlineprivate

References test.T220_AtomAtomPairEnergies::fa_elec, and basic::options::OptionKeys::frags::scoring::scoring.

ramp_score_weight()

void DockGlycansProtocol::ramp_score_weight ( core::scoring::ScoreType const  method, core::Real const  target, core::Real const  fraction_completion  )

inlineprivate

References basic::options::OptionKeys::sasa::method, and basic::options::OptionKeys::hotspot::target.

record_pose_metrics()

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, bin_torsions::job, ligand_rmsd(), beta_nonlocal::pose, and basic::options::OptionKeys::frags::scoring::scoring.

register_options()

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, and register_options().

score_function()

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

inline

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

set_commandline_options()

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, and option.

set_ref_pose_from_filename()

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

inline

References lactamize::filename, and pyrosetta.distributed.io::pose_from_file.

show()

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

inlineoverride

Generate string representation of DockGlycansProtocol for debugging purposes.

References bin_torsions::output, and show().

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

Member Data Documentation

atr_mult_

core::Real DockGlycansProtocol::atr_mult_

private

Referenced by copy_data().

constraint_setter_

protocols::constraint_movers::ConstraintSetMoverOP DockGlycansProtocol::constraint_setter_

private

Referenced by copy_data().

downstream_chains_

std::string DockGlycansProtocol::downstream_chains_

private

Referenced by copy_data().

elec_mult_

core::Real DockGlycansProtocol::elec_mult_

private

Referenced by copy_data().

first_ligand_residue_

core::uint DockGlycansProtocol::first_ligand_residue_

private

Referenced by copy_data().

Hbond_mult_

core::Real DockGlycansProtocol::Hbond_mult_

private

Referenced by copy_data().

idealize_rings_

bool DockGlycansProtocol::idealize_rings_

private

Referenced by copy_data().

jump_minimizer_

protocols::minimization_packing::MinMoverOP DockGlycansProtocol::jump_minimizer_

private

Referenced by copy_data().

jump_mm_

core::kinematics::MoveMapOP DockGlycansProtocol::jump_mm_

private

Referenced by copy_data().

JUMP_NUM

core::uint const DockGlycansProtocol::JUMP_NUM

staticprivate

kt_

core::Real DockGlycansProtocol::kt_

private

Referenced by copy_data().

lock_rings_

bool DockGlycansProtocol::lock_rings_

private

Referenced by copy_data().

mc_

protocols::moves::MonteCarloOP DockGlycansProtocol::mc_

private

Referenced by copy_data().

n_cycles_

core::Size DockGlycansProtocol::n_cycles_

private

Referenced by copy_data().

packer_

protocols::minimization_packing::PackRotamersMoverOP DockGlycansProtocol::packer_

private

Referenced by copy_data().

perturber_

protocols::rigid::RigidBodyPerturbMoverOP DockGlycansProtocol::perturber_

private

Referenced by copy_data().

randomizerA_

protocols::rigid::RigidBodyRandomizeMoverOP DockGlycansProtocol::randomizerA_

private

Referenced by copy_data().

ref_pose_

core::pose::PoseOP DockGlycansProtocol::ref_pose_

private

Referenced by copy_data().

rep_mult_

core::Real DockGlycansProtocol::rep_mult_

private

Referenced by copy_data().

ring_mm_

core::kinematics::MoveMapOP DockGlycansProtocol::ring_mm_

private

Referenced by copy_data().

ring_mover_

protocols::simple_moves::RingConformationMoverOP DockGlycansProtocol::ring_mover_

private

Referenced by copy_data().

rot_

core::Angle DockGlycansProtocol::rot_

private

Referenced by copy_data().

sf_

core::scoring::ScoreFunctionOP DockGlycansProtocol::sf_

private

Referenced by copy_data().

shear_mover_

protocols::simple_moves::ShearMoverOP DockGlycansProtocol::shear_mover_

private

Referenced by copy_data().

slider_

protocols::docking::FaDockingSlideIntoContactOP DockGlycansProtocol::slider_

private

Referenced by copy_data().

small_mover_

protocols::simple_moves::SmallMoverOP DockGlycansProtocol::small_mover_

private

Referenced by copy_data().

sol_mult_

core::Real DockGlycansProtocol::sol_mult_

private

Referenced by copy_data().

STARTING_RAMP_DOWN_FACTOR

core::Real const DockGlycansProtocol::STARTING_RAMP_DOWN_FACTOR

staticprivate

STARTING_RAMP_UP_FACTOR

core::Real const DockGlycansProtocol::STARTING_RAMP_UP_FACTOR

staticprivate

target_atr_

core::Real DockGlycansProtocol::target_atr_

private

Referenced by copy_data().

target_rep_

core::Real DockGlycansProtocol::target_rep_

private

Referenced by copy_data().

torsion_minimizer_

protocols::minimization_packing::MinMoverOP DockGlycansProtocol::torsion_minimizer_

private

Referenced by copy_data().

torsion_mm_

core::kinematics::MoveMapOP DockGlycansProtocol::torsion_mm_

private

Referenced by copy_data().

trans_

core::Distance DockGlycansProtocol::trans_

private

Referenced by copy_data().

upstream_chains_

std::string DockGlycansProtocol::upstream_chains_

private

Referenced by copy_data().

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

• src/apps/public/carbohydrates/dock_glycans.cc