#include <GlycanDockProtocol.hh>

Inheritance diagram for protocols::glycan_docking::GlycanDockProtocol:

[legend]

Public Member Functions
	GlycanDockProtocol ()
	Constructors ///. More...

	GlycanDockProtocol (GlycanDockProtocol const &object_to_copy)
	Copy constructor for deep copies. More...

	~GlycanDockProtocol () override
	Assignment operator. More...

void	apply (core::pose::Pose &pose) override
	Mover Methods ///. More...

void	show (std::ostream &output) const override
	Generate string representation of GlycanDockProtocol. More...

void	show () const
	PyRosetta-friendly version of show. More...

void	parse_my_tag (utility::tag::TagCOP tag, basic::datacache::DataMap &data) override
	Rosetta Scripts Support ///. 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_scorefunction (core::scoring::ScoreFunctionOP const &in_sf)
	Setter Methods //. More...

void	set_n_repeats (core::Size const &n_repeats)
	Set the number of times to repeat the GlycanDockProtocol. More...

void	set_refine_only (bool const refine_only)
	Set whether to skip Stage 1 of GlycanDockProtocol and perform more. More...

void	set_prepack_only (bool const prepack_only)
	Set whether to apply only the GlycanDock pre-packing protocol. More...

void	set_partners (std::string const &p)
	Set the chain IDs identifying the protein-glycoligand complex. More...

void	set_stage1_rotate_glycan_about_com (bool const sg1)
	Set whether the Stage 1 conformation initialization portion. More...

void	set_stage1_perturb_glycan_com_trans_mag (core::Real const trans_mag)
	Set the magnitude used when applying a random translational. More...

void	set_stage1_perturb_glycan_com_rot_mag (core::Real const rot_mag)
	Set the magnitude used when applying a random rotational. More...

void	set_stage1_torsion_uniform_pert_mag (core::Real const pert_mag)
	Set the magnitude used when applying a random perturbation to. More...

void	set_n_rigid_body_rounds (core::Size const rb_rounds)
	Set the number of rigid-body sampling and optimization. More...

void	set_slide_glycan_into_contact (bool const slide)
	Set wehter to ocassionally rigidly slide the glycoligand. More...

void	set_n_torsion_rounds (core::Size const tor_rounds)
	Set the number of glycosidic torsion angle sampling and optimization. More...

void	set_stage2_trans_mag (core::Real const trans_mag)
	Set the magnitude used when applying a random translational. More...

void	set_stage2_rot_mag (core::Real const rot_mag)
	Set the magnitude used when applying a random rotational. More...

void	set_rand_glycan_jump_res (bool const rand_glyc_jump)
	Set whether to use a random, non-branch-point residue of the. More...

void	set_mc_kt (core::Real const mc_kt)
	Set the temperature (kT) used when applying the Metropolis. More...

void	set_full_packing_frequency (core::Size const full_pack_freq)
	Set the number of times to apply the more costly PackRotamersMover. More...

void	set_interface_packing_distance (core::Real const intf_pack_dist)
	Set the distance in Ang. defining the protein-glycoligand interface. More...

void	set_ramp_scorefxn (bool const ramp_sf)
	Set whether to ramp the fa_atr and fa_rep score terms of the. More...

void	set_watch_in_pymol (bool const pymol)
	Send the conformation of the decoy to PyMOL at specific,. More...

core::scoring::ScoreFunctionOP const	get_scorefunction ()
	Getter Methods //. More...

core::Size	get_n_repeats ()
	Get the number of times to repeat the GlycanDockProtocol. More...

bool	get_refine_only ()
	Get whether to skip Stage 1 of GlycanDockProtocol and perform more. More...

bool	get_prepack_only ()
	Get whether to apply only the GlycanDock pre-packing protocol. More...

std::string	get_partners () const
	Get the chain IDs identifying the protein-glycoligand complex. More...

bool	get_stage1_rotate_glycan_about_com ()
	Get whether the Stage 1 conformation initialization portion. More...

core::Real	get_stage1_perturb_glycan_com_trans_mag ()
	Get the magnitude used when applying a random translational. More...

core::Real	get_stage1_perturb_glycan_com_rot_mag ()
	Get the magnitude used when applying a random rotational. More...

core::Real	get_stage1_torsion_uniform_pert_mag ()
	Get the magnitude used when applying a random perturbation to. More...

core::Size	get_n_rigid_body_rounds ()
	Get the number of rigid-body sampling and optimization. More...

bool	get_slide_glycan_into_contact ()
	Get wehter to ocassionally rigidly slide the glycoligand. More...

core::Size	get_n_torsion_rounds ()
	Get the number of glycosidic torsion angle sampling and optimization. More...

core::Real	get_stage2_trans_mag ()
	Get the magnitude used when applying a random translational. More...

core::Real	get_stage2_rot_mag ()
	Get the magnitude used when applying a random rotational. More...

bool	get_rand_glycan_jump_res ()
	Get whether to use a random, non-branch-point residue of the. More...

core::Real	get_mc_kt ()
	Get the temperature (kT) used when applying the Metropolis. More...

core::Size	get_full_packing_frequency ()
	Get the number of times to apply the more costly PackRotamersMover. More...

core::Real	get_interface_packing_distance ()
	Get the distance in Ang. defining the protein-glycoligand interface. More...

bool	get_ramp_scorefxn ()
	Get whether to ramp the fa_atr and fa_rep score terms of the. More...

bool	get_watch_in_pymol ()
	Send the conformation of the decoy to PyMOL at specific,. More...

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

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 Strings &	info ()
	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 void	provide_xml_schema (utility::tag::XMLSchemaDefinition &xsd)

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	register_options ()
	Setup Methods ///. More...

void	set_defaults ()
	Setup defaults not managed by flags at construction. More...

void	set_cmd_line_defaults ()
	Initialize additional command-line options specified by user. More...

void	init_options ()
	Set protocol values from command line upon construction. More...

void	clear_counters ()
	Copy protocol data. More...

void	setup_scorefxn (core::pose::Pose &pose)
	Prepare scoring function with necessary sugar score terms Also stores target weights for fa_atr and fa_rep for ramping. More...

void	setup_docking_foldtree (core::pose::Pose &pose, core::pose::Pose &ref_pose)
	Setup function for preparing FoldTree for glycoligand docking By default, a random (non branch point) carbohydrate residue will be selected as the downstream Jump residue. More...

void	ramp_score_weight (core::scoring::ScoreType const score_type, core::Real const target_weight, core::Size const current_cycle, core::Size const n_cycles)
	Set the weight for the specified ScoreType in the ScoreFunction Score ramping based on ramping factor and fraction of protocol completion. More...

void	perform_stage2_docking_and_optimization (core::pose::Pose &pose, protocols::moves::RandomMoverOP stage2_rb_randmover, protocols::moves::RandomMoverOP stage2_tor_randmover, minimization_packing::PackRotamersMoverOP full_packer, minimization_packing::EnergyCutRotamerTrialsMoverOP ecut_packer, minimization_packing::MinMoverOP min_mover, moves::MonteCarloOP mc)
	Stage 2 docking refinement portion of the GlycanDockProtocol Performs inner cycles of n_rb_rounds_ of rigid-body perturbations and n_tor_rounds_ of glycosidic torsion angle perturbation Calling this function is considered one inner cycle of Stage 2 Packing is performed after every perturbation, where the ecut_packer is called every time the full_packer is not, and the full_packer is is called after every full_pack_req_ moves Example: n_rb_rounds_ = n_tor_rounds_ = 8; full_pack_freq_ = 8 Minimization is called after every other perturbation. More...

bool	docking_filter (core::pose::Pose const &pose, core::Size const repeat)
	Check decoy score to determine if it passed the docking filter Default filter is checking if the decoy has an interaction_energy < 0. More...

void	record_pose_metrics (core::pose::Pose &pose, utility::vector1< bool > const &glycolig_subset, core::pose::Pose const &ref_pose, utility::vector1< bool > const &ref_glycolig_subset)
	Record a collection of decoy metrics. More...

void	record_protocol_info (core::pose::Pose &pose)
	Relay and record protocol-level GlycanDock results. More...

void	prepack_only (core::pose::Pose &pose, protocols::minimization_packing::PackRotamersMoverOP prepack_packer)
	Prepack protocol for GlycanDock (based on FlexPepDock prepack) (1) translate glycoligand away (by 1000 Ang) (2) independently pack all side-chains (3) translate glycoligand back to starting position. More...

Private Attributes
utility::pointer::DeepCopyOP< core::scoring::ScoreFunction >	scorefxn_

core::Real	mc_kt_ = 0.6

bool	ramp_scorefxn_ = true

core::Real	target_atr_ = 1

core::Real	target_rep_ = 0.55

core::Real	starting_ramp_down_atr_factor_ = 3.25

core::Real	starting_ramp_up_rep_factor_ = 0.45455

core::Size	full_pack_freq_ = 8

core::Real const	rt_energycut_ = 0.05

bool	lock_rings_ = true

std::string	min_type_ = "lbfgs_armijo_nonmonotone"

core::Real	min_tolerance_ = 0.01

core::Size	n_cycles_ = 10

core::Size	n_repeats_ = 3

std::string	partners_ = "_"

bool	partners_provided_ = false

core::Real	intf_pack_dist_ = 16

bool	rand_glyc_jump_res_ = true

core::Size	dock_jump_num_ = 1

protocols::docking::DockJumps	movable_jump_

bool	prepack_only_ = false

bool	refine_only_ = false

bool	watch_in_pymol_ = false

bool	glycoligand_has_dihedrals_ = true

core::Real	stage1_trans_mag_ = 0.5

core::Real	stage1_rot_mag_ = 7.5

bool	stage1_rotate_glyc_about_com_ = false

core::Real	stage1_torsion_uniform_pert_mag_ = 12.5

core::Size	n_rb_rounds_ = 8

core::Real	stage2_trans_mag_ = 0.5

core::Real	stage2_rot_mag_ = 7.5

bool	slide_glyc_into_contact_ = true

core::Size	n_tor_rounds_ = 8

core::Size	n_shear_moves_ = 1

core::Size	n_rb_moves_made_ = 0

core::Size	n_rb_moves_accepted_ = 0

core::Size	n_rb_cycles_performed_ = 0

core::Size	n_tor_moves_made_ = 0

core::Size	n_tor_moves_accepted_ = 0

core::Size	n_tor_cycles_performed_ = 0

core::Size	n_stage2_cycles_performed_ = 0

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

TODO.

Author: Morgan L. Nance (@mlnance)

Constructor & Destructor Documentation

◆ GlycanDockProtocol() [1/2]

protocols::glycan_docking::GlycanDockProtocol::GlycanDockProtocol ( )

Constructors ///.

Default constructor.

Default GlycanDock constructor

References register_options(), set_defaults(), and protocols::moves::Mover::type().

◆ GlycanDockProtocol() [2/2]

protocols::glycan_docking::GlycanDockProtocol::GlycanDockProtocol ( GlycanDockProtocol const & object_to_copy )

default

Copy constructor for deep copies.

Copy constructor.

◆ ~GlycanDockProtocol()

protocols::glycan_docking::GlycanDockProtocol::~GlycanDockProtocol ( )

override

Assignment operator.

Destructor

Member Function Documentation

◆ apply()

void protocols::glycan_docking::GlycanDockProtocol::apply ( core::pose::Pose & pose )

overridevirtual

Mover Methods ///.

Apply the GlycanDockProtocol mover

Implements protocols::moves::Mover.

◆ clear_counters()

void protocols::glycan_docking::GlycanDockProtocol::clear_counters ( )

private

Copy protocol data.

Protocol Methods ///

Reset counters used for diagnostic purposes during docking

References n_rb_cycles_performed_, n_rb_moves_accepted_, n_rb_moves_made_, n_stage2_cycles_performed_, n_tor_cycles_performed_, n_tor_moves_accepted_, n_tor_moves_made_, and protocols::TR().

Referenced by apply(), and set_defaults().

◆ clone()

protocols::moves::MoverOP protocols::glycan_docking::GlycanDockProtocol::clone ( ) const

overridevirtual

required in the context of the parser/scripting scheme

Reimplemented from protocols::moves::Mover.

◆ docking_filter()

bool protocols::glycan_docking::GlycanDockProtocol::docking_filter	(	core::pose::Pose const &	pose,
		core::Size const	repeat
	)

private

Check decoy score to determine if it passed the docking filter Default filter is checking if the decoy has an interaction_energy < 0.

References protocols::docking::calc_interaction_energy(), movable_jump_, n_repeats_, scorefxn_, and protocols::TR().

Referenced by apply().

◆ fresh_instance()

protocols::moves::MoverOP protocols::glycan_docking::GlycanDockProtocol::fresh_instance ( ) const

overridevirtual

required in the context of the parser/scripting scheme

Reimplemented from protocols::moves::Mover.

◆ get_full_packing_frequency()

core::Size protocols::glycan_docking::GlycanDockProtocol::get_full_packing_frequency ( )

inline

Get the number of times to apply the more costly PackRotamersMover.

during the inner cycles of Stage 2 sampling and optimization.

Should be a factor of n_rb_rounds and n_tor_rounds. When the

PackRotamersMover is not used, the EnergyCutRotamerTrialsMover is

References full_pack_freq_.

◆ get_interface_packing_distance()

core::Real protocols::glycan_docking::GlycanDockProtocol::get_interface_packing_distance ( )

inline

Get the distance in Ang. defining the protein-glycoligand interface.

when performing packing during Stage 2 sampling and optimization

Note: Uses less accurate neighbor atom distances to get interface

References intf_pack_dist_.

◆ get_mc_kt()

core::Real protocols::glycan_docking::GlycanDockProtocol::get_mc_kt ( )

inline

Get the temperature (kT) used when applying the Metropolis.

criterion via the MonteCarlo object to accept or a reject a move

References mc_kt_.

◆ get_n_repeats()

core::Size protocols::glycan_docking::GlycanDockProtocol::get_n_repeats ( )

inline

Get the number of times to repeat the GlycanDockProtocol.

starting from the decoy conformation after Stage 1 (if applied)

if the decoy fails the docking filter at the end of the protocol

References n_repeats_.

◆ get_n_rigid_body_rounds()

core::Size protocols::glycan_docking::GlycanDockProtocol::get_n_rigid_body_rounds ( )

inline

Get the number of rigid-body sampling and optimization.

rounds to perform during each inner cycle of Stage 2

References n_rb_rounds_.

◆ get_n_torsion_rounds()

core::Size protocols::glycan_docking::GlycanDockProtocol::get_n_torsion_rounds ( )

inline

Get the number of glycosidic torsion angle sampling and optimization.

rounds to perform during each inner cycle of Stage 2

References n_tor_rounds_.

◆ get_name()

std::string protocols::glycan_docking::GlycanDockProtocol::get_name ( ) const

overridevirtual

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

Implements protocols::moves::Mover.

References mover_name().

◆ get_partners()

std::string protocols::glycan_docking::GlycanDockProtocol::get_partners ( ) const

inline

Get the chain IDs identifying the protein-glycoligand complex.

protein is chain A, glycoligand is chain X --> partners = A_X

References partners_.

◆ get_prepack_only()

bool protocols::glycan_docking::GlycanDockProtocol::get_prepack_only ( )

inline

Get whether to apply only the GlycanDock pre-packing protocol.

References prepack_only_.

◆ get_ramp_scorefxn()

bool protocols::glycan_docking::GlycanDockProtocol::get_ramp_scorefxn ( )

inline

Get whether to ramp the fa_atr and fa_rep score terms of the.

ScoreFunction used during Stage 2 sampling and optimization

References ramp_scorefxn_.

◆ get_rand_glycan_jump_res()

bool protocols::glycan_docking::GlycanDockProtocol::get_rand_glycan_jump_res ( )

inline

Get whether to use a random, non-branch-point residue of the.

glycoligand to set as the Jump residue for the docking FoldTree

References rand_glyc_jump_res_.

◆ get_refine_only()

bool protocols::glycan_docking::GlycanDockProtocol::get_refine_only ( )

inline

Get whether to skip Stage 1 of GlycanDockProtocol and perform more.

conservative glycosidic torsion angle moves during Stage 2

References refine_only_.

◆ get_scorefunction()

core::scoring::ScoreFunctionOP const protocols::glycan_docking::GlycanDockProtocol::get_scorefunction ( )

inline

Getter Methods //.

Get the ScoreFunction used for the GlycanDockProtocol

References scorefxn_.

◆ get_slide_glycan_into_contact()

bool protocols::glycan_docking::GlycanDockProtocol::get_slide_glycan_into_contact ( )

inline

Get wehter to ocassionally rigidly slide the glycoligand.

toward the center-of-mass of its proteein docking partner

during Stage 2 rigid-body sampling and optimization cycles

References slide_glyc_into_contact_.

◆ get_stage1_perturb_glycan_com_rot_mag()

core::Real protocols::glycan_docking::GlycanDockProtocol::get_stage1_perturb_glycan_com_rot_mag ( )

inline

Get the magnitude used when applying a random rotational.

perturbation to the initial glycoligand conformation in Stage 1

References stage1_rot_mag_.

◆ get_stage1_perturb_glycan_com_trans_mag()

core::Real protocols::glycan_docking::GlycanDockProtocol::get_stage1_perturb_glycan_com_trans_mag ( )

inline

Get the magnitude used when applying a random translational.

perturbation to the initial glycoligand conformation in Stage 1

References stage1_trans_mag_.

◆ get_stage1_rotate_glycan_about_com()

bool protocols::glycan_docking::GlycanDockProtocol::get_stage1_rotate_glycan_about_com ( )

inline

Get whether the Stage 1 conformation initialization portion.

of the GlycanDockProtocol is performed

References stage1_rotate_glyc_about_com_.

◆ get_stage1_torsion_uniform_pert_mag()

core::Real protocols::glycan_docking::GlycanDockProtocol::get_stage1_torsion_uniform_pert_mag ( )

inline

Get the magnitude used when applying a random perturbation to.

each initial glycosidic torsion angle during Stage 1

References stage1_torsion_uniform_pert_mag_.

◆ get_stage2_rot_mag()

core::Real protocols::glycan_docking::GlycanDockProtocol::get_stage2_rot_mag ( )

inline

Get the magnitude used when applying a random rotational.

perturbation to the glycoligand conformation in Stage 2

References stage2_rot_mag_.

◆ get_stage2_trans_mag()

core::Real protocols::glycan_docking::GlycanDockProtocol::get_stage2_trans_mag ( )

inline

Get the magnitude used when applying a random translational.

perturbation to the glycoligand conformation in Stage 2

References stage2_trans_mag_.

◆ get_watch_in_pymol()

bool protocols::glycan_docking::GlycanDockProtocol::get_watch_in_pymol ( )

inline

Send the conformation of the decoy to PyMOL at specific,.

hard-coded points during the GlycanDockProtocol

Note: TODO - currently not implemented

References watch_in_pymol_.

◆ init_options()

void protocols::glycan_docking::GlycanDockProtocol::init_options ( )

private

Set protocol values from command line upon construction.

◆ mover_name()

std::string protocols::glycan_docking::GlycanDockProtocol::mover_name ( )

static

Referenced by get_name(), protocols::glycan_docking::GlycanDockProtocolCreator::keyname(), and provide_xml_schema().

◆ parse_my_tag()

void protocols::glycan_docking::GlycanDockProtocol::parse_my_tag	(	utility::tag::TagCOP	tag,
		basic::datacache::DataMap &	data
	)

overridevirtual

Rosetta Scripts Support ///.

parse XML tag (to use GlycanDockProtocol in Rosetta Scripts)

parse XML tag

Rosetta Scripts Support ///

Reimplemented from protocols::moves::Mover.

References set_full_packing_frequency(), set_interface_packing_distance(), set_mc_kt(), set_n_repeats(), set_n_rigid_body_rounds(), set_n_torsion_rounds(), set_partners(), set_prepack_only(), set_ramp_scorefxn(), set_refine_only(), set_stage1_perturb_glycan_com_rot_mag(), set_stage1_perturb_glycan_com_trans_mag(), set_stage1_rotate_glycan_about_com(), set_stage1_torsion_uniform_pert_mag(), set_stage2_rot_mag(), set_stage2_trans_mag(), and set_watch_in_pymol().

◆ perform_stage2_docking_and_optimization()

void protocols::glycan_docking::GlycanDockProtocol::perform_stage2_docking_and_optimization	(	core::pose::Pose &	pose,
		protocols::moves::RandomMoverOP	stage2_rb_randmover,
		protocols::moves::RandomMoverOP	stage2_tor_randmover,
		minimization_packing::PackRotamersMoverOP	full_packer,
		minimization_packing::EnergyCutRotamerTrialsMoverOP	ecut_packer,
		minimization_packing::MinMoverOP	min_mover,
		moves::MonteCarloOP	mc
	)

private

Stage 2 docking refinement portion of the GlycanDockProtocol Performs inner cycles of n_rb_rounds_ of rigid-body perturbations and n_tor_rounds_ of glycosidic torsion angle perturbation Calling this function is considered one inner cycle of Stage 2 Packing is performed after every perturbation, where the ecut_packer is called every time the full_packer is not, and the full_packer is is called after every full_pack_req_ moves Example: n_rb_rounds_ = n_tor_rounds_ = 8; full_pack_freq_ = 8 Minimization is called after every other perturbation.

References protocols::glycan_docking::do_stage2_sample_pack_min_cycle(), full_pack_freq_, glycoligand_has_dihedrals_, n_rb_cycles_performed_, n_rb_moves_accepted_, n_rb_moves_made_, n_rb_rounds_, n_stage2_cycles_performed_, n_tor_cycles_performed_, n_tor_moves_accepted_, n_tor_moves_made_, n_tor_rounds_, and core::scoring::rg.

Referenced by apply().

◆ prepack_only()

void protocols::glycan_docking::GlycanDockProtocol::prepack_only	(	core::pose::Pose &	pose,
		protocols::minimization_packing::PackRotamersMoverOP	prepack_packer
	)

private

Prepack protocol for GlycanDock (based on FlexPepDock prepack) (1) translate glycoligand away (by 1000 Ang) (2) independently pack all side-chains (3) translate glycoligand back to starting position.

References protocols::rigid::RigidBodyTransMover::apply(), dock_jump_num_, protocols::rigid::RigidBodyTransMover::step_size(), protocols::TR(), and protocols::rigid::RigidBodyTransMover::trans_axis().

Referenced by apply(), set_prepack_only(), and show().

◆ provide_xml_schema()

void protocols::glycan_docking::GlycanDockProtocol::provide_xml_schema ( utility::tag::XMLSchemaDefinition & xsd )

static

References mover_name(), and protocols::moves::xsd_type_definition_w_attributes().

Referenced by protocols::glycan_docking::GlycanDockProtocolCreator::provide_xml_schema().

◆ ramp_score_weight()

void protocols::glycan_docking::GlycanDockProtocol::ramp_score_weight	(	core::scoring::ScoreType const	score_type,
		core::Real const	target_weight,
		core::Size const	current_cycle,
		core::Size const	n_cycles
	)

private

Set the weight for the specified ScoreType in the ScoreFunction Score ramping based on ramping factor and fraction of protocol completion.

Note: Assumes that only fa_atr and fa_rep are being ramped

References core::scoring::fa_atr, core::scoring::fa_rep, scorefxn_, starting_ramp_down_atr_factor_, starting_ramp_up_rep_factor_, target_atr_, target_rep_, core::id::to_string(), and protocols::TR().

Referenced by apply().

◆ record_pose_metrics()

void protocols::glycan_docking::GlycanDockProtocol::record_pose_metrics	(	core::pose::Pose &	pose,
		utility::vector1< bool > const &	glycolig_subset,
		core::pose::Pose const &	ref_pose,
		utility::vector1< bool > const &	ref_glycolig_subset
	)

private

Record a collection of decoy metrics.

References protocols::glycan_docking::calc_GlycanDock_intf_metrics(), protocols::docking::calc_interaction_energy(), dock_jump_num_, core::pose::Pose::fold_tree(), core::select::get_residues_from_subset(), core::scoring::is_carbohydrate_ring_atom(), core::scoring::is_heavyatom(), core::kinematics::FoldTree::jump_edge(), movable_jump_, core::scoring::rmsd_no_super(), core::scoring::rmsd_with_super(), scorefxn_, core::pose::setPoseExtraScore(), core::kinematics::Edge::stop(), core::scoring::total_score, and protocols::TR().

Referenced by apply().

◆ record_protocol_info()

void protocols::glycan_docking::GlycanDockProtocol::record_protocol_info ( core::pose::Pose & pose )

private

Relay and record protocol-level GlycanDock results.

References n_rb_cycles_performed_, n_rb_moves_accepted_, n_rb_moves_made_, n_stage2_cycles_performed_, n_tor_cycles_performed_, n_tor_moves_accepted_, n_tor_moves_made_, core::pose::setPoseExtraScore(), and protocols::TR().

Referenced by apply().

◆ register_options()

void protocols::glycan_docking::GlycanDockProtocol::register_options ( )

private

Setup Methods ///.

Register options for Movers relevant to GlycanDockProtocol.

Register options from command line upon construction

References protocols::carbohydrates::RingPlaneFlipMover::register_options(), protocols::constraint_movers::ConstraintSetMover::register_options(), and protocols::moves::Mover::register_options().

Referenced by GlycanDockProtocol().

◆ set_cmd_line_defaults()

void protocols::glycan_docking::GlycanDockProtocol::set_cmd_line_defaults ( )

private

Initialize additional command-line options specified by user.

References full_pack_freq_, intf_pack_dist_, lock_rings_, mc_kt_, min_tolerance_, min_type_, n_cycles_, n_rb_rounds_, n_repeats_, n_tor_rounds_, partners_, partners_provided_, prepack_only_, ramp_scorefxn_, rand_glyc_jump_res_, refine_only_, slide_glyc_into_contact_, stage1_rot_mag_, stage1_rotate_glyc_about_com_, stage1_torsion_uniform_pert_mag_, stage1_trans_mag_, stage2_rot_mag_, stage2_trans_mag_, and watch_in_pymol_.

Referenced by set_defaults().

◆ set_defaults()

void protocols::glycan_docking::GlycanDockProtocol::set_defaults ( )

private

Setup defaults not managed by flags at construction.

References clear_counters(), dock_jump_num_, movable_jump_, and set_cmd_line_defaults().

Referenced by GlycanDockProtocol().

◆ set_full_packing_frequency()

void protocols::glycan_docking::GlycanDockProtocol::set_full_packing_frequency ( core::Size const full_pack_freq )

inline

Set the number of times to apply the more costly PackRotamersMover.

during the inner cycles of Stage 2 sampling and optimization.

Should be a factor of n_rb_rounds and n_tor_rounds. When the

PackRotamersMover is not used, the EnergyCutRotamerTrialsMover is

References full_pack_freq_.

Referenced by parse_my_tag().

◆ set_interface_packing_distance()

void protocols::glycan_docking::GlycanDockProtocol::set_interface_packing_distance ( core::Real const intf_pack_dist )

inline

Set the distance in Ang. defining the protein-glycoligand interface.

when performing packing during Stage 2 sampling and optimization

Note: Uses less accurate neighbor atom distances to get interface

References intf_pack_dist_.

Referenced by parse_my_tag().

◆ set_mc_kt()

void protocols::glycan_docking::GlycanDockProtocol::set_mc_kt ( core::Real const mc_kt )

inline

Set the temperature (kT) used when applying the Metropolis.

criterion via the MonteCarlo object to accept or a reject a move

References mc_kt_.

Referenced by parse_my_tag().

◆ set_n_repeats()

void protocols::glycan_docking::GlycanDockProtocol::set_n_repeats ( core::Size const & n_repeats )

inline

Set the number of times to repeat the GlycanDockProtocol.

starting from the decoy conformation after Stage 1 (if applied)

if the decoy fails the docking filter at the end of the protocol

References n_repeats_.

Referenced by parse_my_tag().

◆ set_n_rigid_body_rounds()

void protocols::glycan_docking::GlycanDockProtocol::set_n_rigid_body_rounds ( core::Size const rb_rounds )

inline

Set the number of rigid-body sampling and optimization.

rounds to perform during each inner cycle of Stage 2

References n_rb_rounds_.

Referenced by parse_my_tag().

◆ set_n_torsion_rounds()

void protocols::glycan_docking::GlycanDockProtocol::set_n_torsion_rounds ( core::Size const tor_rounds )

inline

Set the number of glycosidic torsion angle sampling and optimization.

rounds to perform during each inner cycle of Stage 2

References n_tor_rounds_.

Referenced by parse_my_tag().

◆ set_partners()

void protocols::glycan_docking::GlycanDockProtocol::set_partners ( std::string const & p )

inline

Set the chain IDs identifying the protein-glycoligand complex.

protein is chain A, glycoligand is chain X --> partners = A_X

References partners_.

Referenced by parse_my_tag().

◆ set_prepack_only()

void protocols::glycan_docking::GlycanDockProtocol::set_prepack_only ( bool const prepack_only )

inline

Set whether to apply only the GlycanDock pre-packing protocol.

References prepack_only(), and prepack_only_.

Referenced by parse_my_tag().

◆ set_ramp_scorefxn()

void protocols::glycan_docking::GlycanDockProtocol::set_ramp_scorefxn ( bool const ramp_sf )

inline

Set whether to ramp the fa_atr and fa_rep score terms of the.

ScoreFunction used during Stage 2 sampling and optimization

References ramp_scorefxn_.

Referenced by parse_my_tag().

◆ set_rand_glycan_jump_res()

void protocols::glycan_docking::GlycanDockProtocol::set_rand_glycan_jump_res ( bool const rand_glyc_jump )

inline

Set whether to use a random, non-branch-point residue of the.

glycoligand to set as the Jump residue for the docking FoldTree

References rand_glyc_jump_res_.

◆ set_refine_only()

void protocols::glycan_docking::GlycanDockProtocol::set_refine_only ( bool const refine_only )

inline

Set whether to skip Stage 1 of GlycanDockProtocol and perform more.

conservative glycosidic torsion angle moves during Stage 2

References refine_only_.

Referenced by parse_my_tag().

◆ set_scorefunction()

void protocols::glycan_docking::GlycanDockProtocol::set_scorefunction ( core::scoring::ScoreFunctionOP const & in_sf )

inline

Setter Methods //.

Set the ScoreFunction used for the GlycanDockProtocol GlycanDock was benchmarked using the ref2015 scoring function with sugar_bb = 0.5 and fa_intra_rep_nonprotein 0.55 (fa_rep weight)

References scorefxn_.

◆ set_slide_glycan_into_contact()

void protocols::glycan_docking::GlycanDockProtocol::set_slide_glycan_into_contact ( bool const slide )

inline

Set wehter to ocassionally rigidly slide the glycoligand.

toward the center-of-mass of its proteein docking partner

during Stage 2 rigid-body sampling and optimization cycles

References slide_glyc_into_contact_.

◆ set_stage1_perturb_glycan_com_rot_mag()

void protocols::glycan_docking::GlycanDockProtocol::set_stage1_perturb_glycan_com_rot_mag ( core::Real const rot_mag )

inline

Set the magnitude used when applying a random rotational.

perturbation to the initial glycoligand conformation in Stage 1

References stage1_rot_mag_.

Referenced by parse_my_tag().

◆ set_stage1_perturb_glycan_com_trans_mag()

void protocols::glycan_docking::GlycanDockProtocol::set_stage1_perturb_glycan_com_trans_mag ( core::Real const trans_mag )

inline

Set the magnitude used when applying a random translational.

perturbation to the initial glycoligand conformation in Stage 1

References stage1_trans_mag_.

Referenced by parse_my_tag().

◆ set_stage1_rotate_glycan_about_com()

void protocols::glycan_docking::GlycanDockProtocol::set_stage1_rotate_glycan_about_com ( bool const sg1 )

inline

Set whether the Stage 1 conformation initialization portion.

of the GlycanDockProtocol is performed

References stage1_rotate_glyc_about_com_.

Referenced by parse_my_tag().

◆ set_stage1_torsion_uniform_pert_mag()

void protocols::glycan_docking::GlycanDockProtocol::set_stage1_torsion_uniform_pert_mag ( core::Real const pert_mag )

inline

Set the magnitude used when applying a random perturbation to.

each initial glycosidic torsion angle during Stage 1

References stage1_torsion_uniform_pert_mag_.

Referenced by parse_my_tag().

◆ set_stage2_rot_mag()

void protocols::glycan_docking::GlycanDockProtocol::set_stage2_rot_mag ( core::Real const rot_mag )

inline

Set the magnitude used when applying a random rotational.

perturbation to the glycoligand conformation in Stage 2

References stage2_rot_mag_.

Referenced by parse_my_tag().

◆ set_stage2_trans_mag()

void protocols::glycan_docking::GlycanDockProtocol::set_stage2_trans_mag ( core::Real const trans_mag )

inline

Set the magnitude used when applying a random translational.

perturbation to the glycoligand conformation in Stage 2

References stage2_trans_mag_.

Referenced by parse_my_tag().

◆ set_watch_in_pymol()

void protocols::glycan_docking::GlycanDockProtocol::set_watch_in_pymol ( bool const pymol )

inline

Send the conformation of the decoy to PyMOL at specific,.

hard-coded points during the GlycanDockProtocol

Note: TODO - currently not implemented

References watch_in_pymol_.

Referenced by parse_my_tag().

◆ setup_docking_foldtree()

void protocols::glycan_docking::GlycanDockProtocol::setup_docking_foldtree	(	core::pose::Pose &	pose,
		core::pose::Pose &	ref_pose
	)

private

Setup function for preparing FoldTree for glycoligand docking By default, a random (non branch point) carbohydrate residue will be selected as the downstream Jump residue.

References core::pose::Pose::fold_tree(), movable_jump_, partners_, rand_glyc_jump_res_, protocols::docking::setup_foldtree(), and protocols::TR().

Referenced by apply().