Main mover for Glycan Relax, which optimizes glycans in a pose. Each round optimizes either one residue for BB sampling, linkage, or multiple for minimization. Currently uses a random sampler with a set of weights to each mover for sampling. More...

#include <GlycanSampler.hh>

Inheritance diagram for protocols::carbohydrates::GlycanSampler:

[legend]

Public Member Functions
	GlycanSampler ()

	GlycanSampler (core::select::residue_selector::ResidueSelectorCOP selector, core::scoring::ScoreFunctionCOP scorefxn, core::Size rounds=75)

	GlycanSampler (GlycanSampler const &src)

	~GlycanSampler () override

void	apply (core::pose::Pose &pose) override
	Main Method. More...

void	provide_citation_info (basic::citation_manager::CitationCollectionList &) const override
	Provide the citation. More...

void	set_residue_selector (core::select::residue_selector::ResidueSelectorCOP selector)
	Set the Movemap. More...

void	set_selector (core::select::residue_selector::ResidueSelectorCOP selector)
	Set a ResidueSelector for glycan residue selection, instead of the typical movemap. More...

void	set_taskfactory (core::pack::task::TaskFactoryCOP tf)
	Set the TaskFactory to control side-chain packing of surrounding amino acids and the OH groups of the glycans. More...

void	set_scorefunction (core::scoring::ScoreFunctionCOP scorefxn)
	Set the ScoreFunction. More...

void	set_rounds (core::Size rounds)
	Each round applys a random mover to pose. This setting is multiplied by the number of glycan residues in the movemap for the total number of rounds. More...

void	set_population_based_conformer_sampling (bool pop_based_sampling)
	Set how our Conformer mover samples. Default is to do uniform sampling on the conformers instead of using the population as probabilities. More...

void	set_use_gaussian_sampling (bool use_gaussian_sampling)
	Set whether if we are sampling torsions uniformly within an SD for the LinkageConformerMover (false) or sampling the gaussian (true). Default false. More...

void	set_kt (core::Real kt)

void	set_defaults ()

void	use_cartmin (bool use_cartmin)
	Use Cartesian minimization instead of Dihedral minimization. Default (for now) is dihedral. More...

void	set_refine (bool refine)
	Set refinement mode instead of denovo modeling mode. More...

void	set_min_rings (bool min_rings)
	set to minimize ring torsions during minimzation. Default false. More...

void	set_use_shear (bool use_shear)
	Set the protocol to use the refactored Shear Mover for glycan torsions at 10 % probability. Default false. More...

void	set_randomize_first (bool randomize_first)
	Set the protocol to randomize torsions before beginning. This actually helps get to lower energy models. Default True. If doing refinement, this is automatically turned off. More...

void	set_inner_bb_cycles (core::Size inner_bb_cycles)
	Set the number of inner cycles for BB sampling through small/sugarBB. This is multiplied by the number of glycan residues Default 1. More...

void	set_protein_linkage_prob_sampling (bool root_probs)
	Set Conformer Sampling through probabilities at the linkage to the protein only. More...

void	show (std::ostream &output=std::cout) const override
	Outputs details about the Mover, including current settings. More...

void	parse_my_tag (utility::tag::TagCOP tag, basic::datacache::DataMap &data) override
	parse XML tag (to use this Mover in Rosetta Scripts) More...

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...

bool	reinitialize_for_each_job () const override
	Inform the Job Distributor (August '08 vintage) whether this object needs to be freshly regenerated on each use. More...

std::string	get_name () const override
	Each derived class must specify its name. The class name. More...

void	randomize_glycan_torsions (core::pose::Pose &pose, utility::vector1< bool > const &subset) const
	Randomize all torsions of the subset. Used to start the protocol. More...

void	idealize_glycan_residues (core::pose::Pose &pose, utility::vector1< core::Size > const &tree_subset) const
	Attempt to idealize all residues in of a set of trees. Experimental! More...

core::Size	get_glycan_sampler_rounds ()
	Get the number of glycan sampler rounds this class is set to run. More...

void	force_total_rounds (core::Size total_rounds)
	This allows us to force a number of rounds instead of doing rounds*glycan residues. 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_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...

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	init_objects (core::pose::Pose &pose)
	Initialize all objects. Called at apply time! More...

void	set_cmd_line_defaults ()

void	apply_to_res (core::pose::Pose &pose, core::Size resnum, core::kinematics::MoveMapOP mm, core::scoring::ScoreFunctionOP score, core::Size round)

void	setup_default_task_factory (utility::vector1< bool > const &glycan_residues, core::pose::Pose const &pose)

void	setup_score_function ()

void	setup_cartmin (core::scoring::ScoreFunctionOP scorefxn) const

void	setup_movers (core::pose::Pose &pose, utility::vector1< bool > const &dihedral_subset, utility::vector1< bool > const &sugar_bb_subset, utility::vector1< bool > const &subset)

void	setup_packer (core::pose::Pose &pose, utility::vector1< bool > const &full_subset)

Private Attributes
core::pack::task::TaskFactoryCOP	tf_ = nullptr

moves::MonteCarloOP	mc_ = nullptr

core::scoring::ScoreFunctionCOP	scorefxn_ = nullptr

LinkageConformerMoverOP	linkage_mover_ = nullptr

moves::RandomMoverOP	weighted_random_mover_ = nullptr

minimization_packing::MinMoverOP	min_mover_ = nullptr

minimization_packing::PackRotamersMoverOP	packer_ = nullptr

simple_moves::ShearMoverOP	shear_ = nullptr

core::Size	rounds_ = 100

core::Real	kt_ = 2.0

utility::vector1< std::string >	accept_log_

bool	test_ = false

bool	final_min_ = true

bool	refine_ = false

core::Size	total_glycan_residues_ = 0

bool	pymol_movie_ = false

utility::vector1< std::string >	parsed_positions_

core::Real	pack_distance_ = 6.0

bool	cartmin_ = false

bool	tree_based_min_pack_ = true

core::select::residue_selector::ResidueSelectorCOP	selector_

bool	population_based_conformer_sampling_ = false

bool	use_gaussian_sampling_ = true

bool	min_rings_ = false

core::Size	forced_total_rounds_ = 0

bool	use_shear_ = true

bool	randomize_first_ = true

core::Size	inner_ncycles_ = 0

bool	match_sampling_of_modeler_ = false

utility::vector1< bool >	final_residue_subset_

bool	root_prob_sampling_ = false

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

Main mover for Glycan Relax, which optimizes glycans in a pose. Each round optimizes either one residue for BB sampling, linkage, or multiple for minimization. Currently uses a random sampler with a set of weights to each mover for sampling.

Weights are currently as follows: .40 Phi/Psi Sugar BB Sampling .20 Linkage Conformer Sampling .30 Small BB Sampling - equal weight to phi, psi, or omega -> .17 +/- 15 degrees -> .086 +/- 45 degrees -> .044 +/- 90 degrees .05 GlycanTreeMinMover .05 PackRotamersMover

Supports Symmetry

Constructor & Destructor Documentation

◆ GlycanSampler() [1/3]

protocols::carbohydrates::GlycanSampler::GlycanSampler ( )

References set_defaults().

◆ GlycanSampler() [2/3]

protocols::carbohydrates::GlycanSampler::GlycanSampler	(	core::select::residue_selector::ResidueSelectorCOP	selector,
		core::scoring::ScoreFunctionCOP	scorefxn,
		core::Size	rounds = `75`
	)

References scorefxn_, selector_, set_defaults(), and set_rounds().

◆ GlycanSampler() [3/3]

protocols::carbohydrates::GlycanSampler::GlycanSampler ( GlycanSampler const & src )

References linkage_mover_, mc_, min_mover_, packer_, scorefxn_, selector_, shear_, tf_, and weighted_random_mover_.

◆ ~GlycanSampler()

protocols::carbohydrates::GlycanSampler::~GlycanSampler ( )

overridedefault

Member Function Documentation

◆ apply()

void protocols::carbohydrates::GlycanSampler::apply ( core::pose::Pose & )

overridevirtual

Main Method.

Implements protocols::moves::Mover.

References accept_log_, core::pose::add_comment(), protocols::moves::PyMOLMover::apply(), protocols::buns::energy, final_min_, final_residue_subset_, forced_total_rounds_, protocols::moves::PyMOLMover::get_PyMOL_model_name(), protocols::carbohydrates::get_total_rounds_for_overlap_one_layer_two(), init_objects(), protocols::moves::PyMOLMover::keep_history(), kt_, match_sampling_of_modeler_, mc_, min_mover_, protocols::moves::MS_SUCCESS, core::conformation::membrane::out, packer_, pymol_movie_, protocols::noesy_assign::round(), rounds_, protocols::carbohydrates::run_shear_min_pack(), scorefxn_, protocols::moves::PyMOLMover::set_PyMOL_model_name(), shear_, core::id::to_string(), total_glycan_residues_, protocols::TR(), use_shear_, and weighted_random_mover_.

Referenced by protocols::carbohydrates::GlycanTreeModeler::apply().

◆ apply_to_res()

void protocols::carbohydrates::GlycanSampler::apply_to_res	(	core::pose::Pose &	pose,
		core::Size	resnum,
		core::kinematics::MoveMapOP	mm,
		core::scoring::ScoreFunctionOP	score,
		core::Size	round
	)

private

◆ clone()

protocols::moves::MoverOP protocols::carbohydrates::GlycanSampler::clone ( ) const

overridevirtual

required in the context of the parser/scripting scheme

Reimplemented from protocols::moves::Mover.

◆ force_total_rounds()

void protocols::carbohydrates::GlycanSampler::force_total_rounds ( core::Size total_rounds )

This allows us to force a number of rounds instead of doing rounds*glycan residues.

References forced_total_rounds_.

Referenced by protocols::carbohydrates::GlycanTreeModeler::apply().

◆ fresh_instance()

moves::MoverOP protocols::carbohydrates::GlycanSampler::fresh_instance ( ) const

overridevirtual

required in the context of the parser/scripting scheme

Reimplemented from protocols::moves::Mover.

◆ get_glycan_sampler_rounds()

core::Size protocols::carbohydrates::GlycanSampler::get_glycan_sampler_rounds ( )

Get the number of glycan sampler rounds this class is set to run.

References rounds_.

Referenced by protocols::carbohydrates::GlycanTreeModeler::apply().

◆ get_name()

std::string protocols::carbohydrates::GlycanSampler::get_name ( ) const

overridevirtual

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

Implements protocols::moves::Mover.

References mover_name().

◆ idealize_glycan_residues()

void protocols::carbohydrates::GlycanSampler::idealize_glycan_residues	(	core::pose::Pose &	pose,
		utility::vector1< core::Size > const &	tree_subset
	)		const

Attempt to idealize all residues in of a set of trees. Experimental!

References protocols::TR().

Referenced by protocols::carbohydrates::GlycanTreeModeler::apply().

◆ init_objects()

void protocols::carbohydrates::GlycanSampler::init_objects ( core::pose::Pose & pose )

private

◆ mover_name()

std::string protocols::carbohydrates::GlycanSampler::mover_name ( )

static

Referenced by get_name(), protocols::carbohydrates::GlycanSamplerCreator::keyname(), provide_citation_info(), and provide_xml_schema().

◆ parse_my_tag()

void protocols::carbohydrates::GlycanSampler::parse_my_tag	(	utility::tag::TagCOP	tag,
		basic::datacache::DataMap &	data
	)

overridevirtual

parse XML tag (to use this Mover in Rosetta Scripts)

Reimplemented from protocols::moves::Mover.

References cartmin_, final_min_, inner_ncycles_, kt_, match_sampling_of_modeler_, min_rings_, pack_distance_, core::select::residue_selector::parse_residue_selector(), core::scoring::parse_score_function(), core::pack::task::parse_task_operations(), population_based_conformer_sampling_, pymol_movie_, randomize_first_, root_prob_sampling_, rounds_, scorefxn_, selector_, set_taskfactory(), tree_based_min_pack_, use_gaussian_sampling_, and use_shear_.

◆ provide_citation_info()

void protocols::carbohydrates::GlycanSampler::provide_citation_info ( basic::citation_manager::CitationCollectionList & citations ) const

overridevirtual

Provide the citation.

Reimplemented from protocols::moves::Mover.

References mover_name().

◆ provide_xml_schema()

void protocols::carbohydrates::GlycanSampler::provide_xml_schema ( utility::tag::XMLSchemaDefinition & xsd )

static

References core::scoring::attributes_for_get_score_function_name(), protocols::rosetta_scripts::attributes_for_parse_residue_selector(), core::pack::task::attributes_for_parse_task_operations(), mover_name(), and protocols::moves::xsd_type_definition_w_attributes_and_repeatable_subelements().

Referenced by protocols::carbohydrates::GlycanSamplerCreator::provide_xml_schema().

◆ randomize_glycan_torsions()

void protocols::carbohydrates::GlycanSampler::randomize_glycan_torsions	(	core::pose::Pose &	pose,
		utility::vector1< bool > const &	subset
	)		const

Randomize all torsions of the subset. Used to start the protocol.

References core::conformation::carbohydrates::get_n_glycosidic_torsions_in_res(), core::pose::Pose::glycan_tree_set(), protocols::simple_moves::bb_sampler::SmallBBSampler::set_torsion_to_pose(), protocols::simple_moves::bb_sampler::BBDihedralSamplerBase::set_torsion_type(), core::pose::Pose::size(), and protocols::TR().

Referenced by protocols::carbohydrates::GlycanTreeModeler::apply(), and init_objects().

◆ reinitialize_for_each_job()

bool protocols::carbohydrates::GlycanSampler::reinitialize_for_each_job ( ) const

inlineoverridevirtual

Inform the Job Distributor (August '08 vintage) whether this object needs to be freshly regenerated on each use.

Movers default to not regenerating

Reimplemented from protocols::moves::Mover.

◆ set_cmd_line_defaults()

void protocols::carbohydrates::GlycanSampler::set_cmd_line_defaults ( )

private

References cartmin_, final_min_, kt_, min_rings_, population_based_conformer_sampling_, pymol_movie_, refine_, rounds_, test_, tree_based_min_pack_, and use_gaussian_sampling_.

Referenced by set_defaults().

◆ set_defaults()

void protocols::carbohydrates::GlycanSampler::set_defaults ( )

References cartmin_, final_min_, pack_distance_, set_cmd_line_defaults(), test_, and total_glycan_residues_.

Referenced by GlycanSampler().

◆ set_inner_bb_cycles()

void protocols::carbohydrates::GlycanSampler::set_inner_bb_cycles ( core::Size inner_bb_cycles )

Set the number of inner cycles for BB sampling through small/sugarBB. This is multiplied by the number of glycan residues Default 1.

References inner_ncycles_.

◆ set_kt()

void protocols::carbohydrates::GlycanSampler::set_kt ( core::Real kt )

References kt_.

Referenced by protocols::carbohydrates::GlycanTreeModeler::apply().

◆ set_min_rings()

void protocols::carbohydrates::GlycanSampler::set_min_rings ( bool min_rings )

set to minimize ring torsions during minimzation. Default false.

References min_rings_.

Referenced by protocols::carbohydrates::GlycanTreeModeler::apply().

◆ set_population_based_conformer_sampling()

void protocols::carbohydrates::GlycanSampler::set_population_based_conformer_sampling ( bool pop_based_sampling )

Set how our Conformer mover samples. Default is to do uniform sampling on the conformers instead of using the population as probabilities.

References population_based_conformer_sampling_.

Referenced by protocols::carbohydrates::GlycanTreeModeler::apply().

◆ set_protein_linkage_prob_sampling()

void protocols::carbohydrates::GlycanSampler::set_protein_linkage_prob_sampling ( bool root_probs )

Set Conformer Sampling through probabilities at the linkage to the protein only.

References root_prob_sampling_.

Referenced by protocols::carbohydrates::GlycanTreeModeler::apply().

◆ set_randomize_first()

void protocols::carbohydrates::GlycanSampler::set_randomize_first ( bool randomize_first )

Set the protocol to randomize torsions before beginning. This actually helps get to lower energy models. Default True. If doing refinement, this is automatically turned off.

References randomize_first_.

Referenced by protocols::carbohydrates::GlycanTreeModeler::apply().

◆ set_refine()

void protocols::carbohydrates::GlycanSampler::set_refine ( bool refine )

Set refinement mode instead of denovo modeling mode.

References refine_.

Referenced by protocols::carbohydrates::GlycanTreeModeler::apply().

◆ set_residue_selector()

void protocols::carbohydrates::GlycanSampler::set_residue_selector ( core::select::residue_selector::ResidueSelectorCOP selector )

Set the Movemap.

References selector_.

◆ set_rounds()

void protocols::carbohydrates::GlycanSampler::set_rounds ( core::Size rounds )

Each round applys a random mover to pose. This setting is multiplied by the number of glycan residues in the movemap for the total number of rounds.

References rounds_.

Referenced by protocols::carbohydrates::GlycanTreeModeler::apply(), and GlycanSampler().

◆ set_scorefunction()

void protocols::carbohydrates::GlycanSampler::set_scorefunction ( core::scoring::ScoreFunctionCOP scorefxn )

Set the ScoreFunction.

References scorefxn_.

Referenced by protocols::carbohydrates::GlycanTreeModeler::apply().

◆ set_selector()

void protocols::carbohydrates::GlycanSampler::set_selector ( core::select::residue_selector::ResidueSelectorCOP selector )

Set a ResidueSelector for glycan residue selection, instead of the typical movemap.

References selector_.

Referenced by protocols::carbohydrates::GlycanTreeModeler::apply().

◆ set_taskfactory()

void protocols::carbohydrates::GlycanSampler::set_taskfactory ( core::pack::task::TaskFactoryCOP tf )

Set the TaskFactory to control side-chain packing of surrounding amino acids and the OH groups of the glycans.

References tf_.

Referenced by parse_my_tag(), and setup_default_task_factory().

◆ set_use_gaussian_sampling()

void protocols::carbohydrates::GlycanSampler::set_use_gaussian_sampling ( bool use_gaussian_sampling )

Set whether if we are sampling torsions uniformly within an SD for the LinkageConformerMover (false) or sampling the gaussian (true). Default false.

References use_gaussian_sampling_.

Referenced by protocols::carbohydrates::GlycanTreeModeler::apply().

◆ set_use_shear()

void protocols::carbohydrates::GlycanSampler::set_use_shear ( bool use_shear )

Set the protocol to use the refactored Shear Mover for glycan torsions at 10 % probability. Default false.

References use_shear_.

Referenced by protocols::carbohydrates::GlycanTreeModeler::apply().

◆ setup_cartmin()

void protocols::carbohydrates::GlycanSampler::setup_cartmin ( core::scoring::ScoreFunctionOP scorefxn ) const

private

References core::scoring::cart_bonded, and core::scoring::pro_close.

Referenced by setup_score_function().

◆ setup_default_task_factory()

void protocols::carbohydrates::GlycanSampler::setup_default_task_factory	(	utility::vector1< bool > const &	glycan_residues,
		core::pose::Pose const &	pose
	)

private

References protocols::carbohydrates::get_all_glycans_and_neighbor_res_task_factory(), core::conformation::Residue::is_virtual_residue(), pack_distance_, core::pose::Pose::residue(), set_taskfactory(), core::pose::Pose::size(), core::pose::Pose::total_residue(), protocols::TR(), and tree_based_min_pack_.

Referenced by setup_packer().

◆ setup_movers()

void protocols::carbohydrates::GlycanSampler::setup_movers	(	core::pose::Pose &	pose,
		utility::vector1< bool > const &	dihedral_subset,
		utility::vector1< bool > const &	sugar_bb_subset,
		utility::vector1< bool > const &	subset
	)