A protocol for optimizing glycan trees using the GlycanSampler from the base of the tree out to the leaves. More...

#include <GlycanTreeModeler.hh>

Inheritance diagram for protocols::carbohydrates::GlycanTreeModeler:

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

	GlycanTreeModeler (GlycanTreeModeler const &src)
	Copy constructor (not needed unless you need deep copies) More...

	~GlycanTreeModeler () override
	Destructor (important for properly forward-declaring smart-pointer members) More...

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

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

void	set_rounds (core::Size const rounds)

void	set_layer_size (core::Size const layer_size)
	Set the layer size we will be using. A layer is a set of glycan residues that we will be optimizing. We work our way through the layers, while the rest of the (downstream) residues are virtual (not scored). More...

void	set_window_size (core::Size const window_size)
	Set the window size. This is the overlap of the layers during modeling. More...

void	set_quench_mode (bool quench_mode)
	Set the protocol to use a quench-like algorithm, where we work on a single glycan tree at a time until all are modeled. More...

void	set_refine (bool const refine)
	Set a boolean that we will be refining instead of de-novo modeling. This also makes it so that modeling is done in the context of the full glycan tree and no virtual residues are used. More...

void	set_final_min_pack_min (bool const minpackmin)
	Change the setting to do a final min/pack/min of all glycan residues or glycan residues set by the selector at the end of the protocol. More...

void	set_glycan_sampler_rounds (core::Size glycan_sampler_rounds)
	Override Glycan Relax rounds. More...

void	set_use_conformer_probabilities (bool conformer_probs)
	Set the LinkageConformer to use probabilites. More...

void	set_use_gaussian_sampling (bool 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_force_virts_for_refinement (bool force_virts)
	Refinement now models layers in the context of the full glycan tree. Turn this option on to use non-scored residues (virtuals) at the ends of the tree that are not being modeled. This is how the de-novo protocol works. More...

void	set_hybrid_protocol (bool hybrid_protocol)
	Set to use an experimental protocol where we build out the glycans, but re-model the full tree during the building process Default false. More...

void	set_use_shear (bool use_shear)

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

void	set_glycan_sampler_kt (core::Real kT)
	Override the GlycanSampler KT. More...

void	set_scorefxn (core::scoring::ScoreFunctionCOP scorefxn)
	Set the scorefunction used for modeling. More...

void	set_selector (core::select::residue_selector::ResidueSelectorCOP selector)
	Set a residue selector to limit the residues we will be modeling. If you are using quench mode, the selector will limit the trees to model. So the residues that are true should correspond to the start of the trees you wish to model. More...

void	show (std::ostream &output=std::cout) const override
	Mover Methods ///. 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...

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...

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	setup_score_function ()

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

bool	is_quenched () const
	Setup classes, selectors, etc. More...

Private Attributes
core::Size	layer_size_ = 1

core::Size	window_size_ = 0

core::Size	rounds_ = 1

core::Size	completed_quenches_ = 0

core::Size	trees_to_model_ = 0

core::Size	glycan_sampler_rounds_ = 100

bool	refine_ = false

bool	quench_mode_ = false

bool	final_min_pack_min_ = true

bool	cartmin_ = false

bool	min_rings_ = false

bool	idealize_ = false

core::scoring::ScoreFunctionOP	scorefxn_ = nullptr

core::select::residue_selector::ResidueSelectorCOP	selector_ = nullptr

bool	use_conformer_populations_ = false

bool	force_virts_for_refine_ = false

bool	hybrid_protocol_ = true

bool	use_gaussian_sampling_ = true

bool	use_shear_ = true

bool	match_window_one_ = true

bool	root_prob_sampling_ = false

core::Real	glycan_sampler_kt_ = 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

A protocol for optimizing glycan trees using the GlycanSampler from the base of the tree out to the leaves.

Works by making all other residues virtual except the ones it is working on (current Layer). A virtual residue is not scored. It will start at the first glycan residues, and then move out to the edges.

GENERAL ALGORITHM

We start at the roots, and make all other glycan residues virtual. We first model towards the leaves and this is considered the forward direction. the GlycanSampler is used for the actual modeling, we only model a layer at a time, until we reach the tips. If more than one round is set, the protocol will move backwards on the next round, from the leafs to the roots. A third round will involve relaxation again in the forward direction. So we go forward, back, forward, etc. for how ever many rounds you set.

QUECHING

By default, we model all glycans simultaneously. First, all glycan roots (the start of the tree), and slowly unvirtualize all glycan residues, while only modeling each layer. Alternatively, we can choose a particular glycan tree, run the algorithm, and then choose another glycan tree randomly until all glycan trees have been optimized. Here, we call this quenching.

GLYCAN LAYERS

Draw a tree on a paper. We start with the beginning N residues, and work our way out towards the leaves. Layers are defined by the glycan residue distance to the rooot. This enables branching residues to be considered the same layer conceptually and computationally, and allows them to be modeled together.

–LAYER SIZE–

The distance that make up a layer. If we have a distance of 2, we first model all glycans that are equal to or less than 2 residue distance to the root. We then slide this layer up. So we take all residues that have a distance between 3 and 1, and so on.

–WINDOW SIZE–

The layers are slid down throught the tree of the glycan. The window size represents the overlap in the layers. A window size of 1, means that the last residue (or residues of layer 1) from the last modeling effort, will be used again as part of the next layer. A window size of 0, means that no residues will be re-modeled. Typically, we would want at least a window size of 1.

Constructor & Destructor Documentation

protocols::carbohydrates::GlycanTreeModeler::GlycanTreeModeler ( )

Constructors ///.

Default constructor

Referenced by clone().

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

Copy constructor (not needed unless you need deep copies)

Copy constructor.

References scorefxn_, and selector_.

protocols::carbohydrates::GlycanTreeModeler::~GlycanTreeModeler ( )

overridedefault

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

Member Function Documentation

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

overridevirtual

Mover Methods ///.

Apply the mover.

Apply the mover

Implements protocols::moves::Mover.

References protocols::minimization_packing::MinMover::apply(), protocols::carbohydrates::backward, cartmin_, core::pose::Pose::clear(), completed_quenches_, core::select::residue_selector::count_selected(), core::pose::carbohydrates::create_glycan_movemap_from_residue_selector(), protocols::moves::FAIL_DO_NOT_RETRY, final_min_pack_min_, force_virts_for_refine_, protocols::carbohydrates::forward, protocols::carbohydrates::get_all_glycans_and_neighbor_res_task_factory(), core::select::get_master_subunit_selection(), protocols::carbohydrates::get_total_rounds_for_overlap_one_layer_two(), glycan_sampler_kt_, glycan_sampler_rounds_, core::pose::Pose::glycan_tree_set(), hybrid_protocol_, idealize_, core::chemical::ResidueType::is_carbohydrate(), core::conformation::Residue::is_carbohydrate(), is_quenched(), core::pose::symmetry::is_symmetric(), layer_size_, match_window_one_, protocols::minimization_packing::MinMover::min_options(), min_rings_, core::pose::Pose::pdb_info(), quench_mode_, core::pose::Pose::real_to_virtual(), refine_, core::pose::Pose::residue(), core::pose::Pose::residue_type(), core::scoring::rg, root_prob_sampling_, protocols::noesy_assign::round(), rounds_, protocols::carbohydrates::run_shear_min_pack(), protocols::minimization_packing::PackRotamersMover::score_function(), scorefxn_, selector_, protocols::moves::Mover::set_last_move_status(), protocols::simple_moves::BackboneMover::set_residue_selector(), setup_score_function(), core::pose::Pose::size(), protocols::minimization_packing::PackRotamersMover::task_factory(), core::id::to_string(), core::pose::Pose::total_residue(), protocols::TR(), trees_to_model_, use_conformer_populations_, use_gaussian_sampling_, use_shear_, and window_size_.

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

overridevirtual

required in the context of the parser/scripting scheme

Reimplemented from protocols::moves::Mover.

References GlycanTreeModeler().

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

overridevirtual

required in the context of the parser/scripting scheme

Reimplemented from protocols::moves::Mover.

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

overridevirtual

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

Implements protocols::moves::Mover.

References mover_name().

bool protocols::carbohydrates::GlycanTreeModeler::is_quenched ( ) const

private

Setup classes, selectors, etc.

References completed_quenches_, quench_mode_, and trees_to_model_.

Referenced by apply().

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

static

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

void protocols::carbohydrates::GlycanTreeModeler::parse_my_tag	(	utility::tag::TagCOP	tag,
		basic::datacache::DataMap &	datamap
	)

overridevirtual

Rosetta Scripts Support ///.

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

Reimplemented from protocols::moves::Mover.

References cartmin_, final_min_pack_min_, force_virts_for_refine_, glycan_sampler_kt_, glycan_sampler_rounds_, hybrid_protocol_, idealize_, layer_size_, match_window_one_, min_rings_, core::select::residue_selector::parse_residue_selector(), core::scoring::parse_score_function(), quench_mode_, refine_, root_prob_sampling_, rounds_, scorefxn_, selector_, set_force_virts_for_refinement(), set_hybrid_protocol(), set_use_conformer_probabilities(), set_use_gaussian_sampling(), use_conformer_populations_, use_gaussian_sampling_, use_shear_, and window_size_.

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

overridevirtual

Provide the citation.

Reimplemented from protocols::moves::Mover.

References mover_name().

void protocols::carbohydrates::GlycanTreeModeler::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(), mover_name(), and protocols::moves::xsd_type_definition_w_attributes().

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

void protocols::carbohydrates::GlycanTreeModeler::set_final_min_pack_min ( bool const minpackmin )

Change the setting to do a final min/pack/min of all glycan residues or glycan residues set by the selector at the end of the protocol.

References final_min_pack_min_.

void protocols::carbohydrates::GlycanTreeModeler::set_force_virts_for_refinement ( bool force_virts )

Refinement now models layers in the context of the full glycan tree. Turn this option on to use non-scored residues (virtuals) at the ends of the tree that are not being modeled. This is how the de-novo protocol works.

References force_virts_for_refine_.

Referenced by parse_my_tag().

void protocols::carbohydrates::GlycanTreeModeler::set_glycan_sampler_kt ( core::Real kT )

Override the GlycanSampler KT.

References glycan_sampler_kt_.

void protocols::carbohydrates::GlycanTreeModeler::set_glycan_sampler_rounds ( core::Size glycan_sampler_rounds )

Override Glycan Relax rounds.

References glycan_sampler_rounds_.

void protocols::carbohydrates::GlycanTreeModeler::set_hybrid_protocol ( bool hybrid_protocol )

Set to use an experimental protocol where we build out the glycans, but re-model the full tree during the building process Default false.

References hybrid_protocol_.

Referenced by parse_my_tag().

void protocols::carbohydrates::GlycanTreeModeler::set_layer_size ( core::Size const layer_size )

Set the layer size we will be using. A layer is a set of glycan residues that we will be optimizing. We work our way through the layers, while the rest of the (downstream) residues are virtual (not scored).

The distance that make up a layer. If we have a distance of 2, we first model all glycans that are equal to or less than 2 residue distance to the root. We then slide this layer up. So we take all residues that have a distance between 3 and 1, and so on.

References layer_size_.

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

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

References root_prob_sampling_.

void protocols::carbohydrates::GlycanTreeModeler::set_quench_mode ( bool quench_mode )

Set the protocol to use a quench-like algorithm, where we work on a single glycan tree at a time until all are modeled.

References quench_mode_.

void protocols::carbohydrates::GlycanTreeModeler::set_refine ( bool const refine )

Set a boolean that we will be refining instead of de-novo modeling. This also makes it so that modeling is done in the context of the full glycan tree and no virtual residues are used.

If you would like to change this behavior, use the function set_force_virts_for_refinement.

References refine_.

void protocols::carbohydrates::GlycanTreeModeler::set_rounds ( core::Size const rounds )

References rounds_.

void protocols::carbohydrates::GlycanTreeModeler::set_scorefxn ( core::scoring::ScoreFunctionCOP scorefxn )

Set the scorefunction used for modeling.

References scorefxn_.

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

Set a residue selector to limit the residues we will be modeling. If you are using quench mode, the selector will limit the trees to model. So the residues that are true should correspond to the start of the trees you wish to model.

If you wish to limit further, this is not currently supported. So email me and I can add it.

References selector_.

void protocols::carbohydrates::GlycanTreeModeler::set_use_conformer_probabilities ( bool conformer_probs )

Set the LinkageConformer to use probabilites.

References use_conformer_populations_.

Referenced by parse_my_tag().

void protocols::carbohydrates::GlycanTreeModeler::set_use_gaussian_sampling ( bool 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 parse_my_tag().

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

References use_shear_.

void protocols::carbohydrates::GlycanTreeModeler::set_window_size ( core::Size const window_size )

Set the window size. This is the overlap of the layers during modeling.

The layers are slid down throught the tree of the glycan. The window size represents the overlap in the layers. A window size of 1, means that the last residue (or residues of layer 1) from the last modeling effort, will be used again as part of the next layer. A window size of 0, means that no residues will be re-modeled. Typically, we would want at least a window size of 1.

References window_size_.

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

private

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

Referenced by setup_score_function().

void protocols::carbohydrates::GlycanTreeModeler::setup_score_function ( )

private

References cartmin_, core::scoring::get_score_function(), scorefxn_, and setup_cartmin().

Referenced by apply().

void protocols::carbohydrates::GlycanTreeModeler::show ( std::ostream & output = std::cout ) const

overridevirtual

Mover Methods ///.