This code changes all of the dihedrals of a particular glycosidic linkage based on database info, esentially sampling carbohydrate dihedral conformers of two residues. Randomly samples on any set selector at each apply or (default) samples a linkage conformer for each residue set. More...

#include <LinkageConformerMover.hh>

Inheritance diagram for protocols::carbohydrates::LinkageConformerMover:

[legend]

Public Member Functions
	LinkageConformerMover ()
	Default constructor. More...

	LinkageConformerMover (core::select::residue_selector::ResidueSelectorCOP selector)
	Constructor with pair of residues in linkage we will build the conformer for. More...

	LinkageConformerMover (LinkageConformerMover const &src)

	~LinkageConformerMover () override

void	set_residue_selector (core::select::residue_selector::ResidueSelectorCOP selector)
	Set the Selector. Each apply will randomly sample Selector. If the conformer is not found, will set move status to false. Will optimize the linkage between the residue and the parent residue. More...

void	set_single_resnum (core::pose::Pose const &pose, core::Size resnum)
	Set a single resnum to sample on instead of a movemap. More...

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

void	set_use_sugar_bb_data_if_needed (bool use_sugar_bb)
	Use phi/psi data if restype-dependant conformer data unavailable. Will set phi/psi to lowest energy values if idealize is true. Default FALSE. More...

void	set_use_gaussian_sampling (bool prob_sd_sample)
	Set whether if we are sampling uniformly within 1 SD or by sampling on the full gaussian directly. Default FALSE. More...

void	set_idealize_torsions (bool idealize_torsions)
	Idealize the torsion angles instead of sampling from SD. Default FALSE. More...

void	set_use_conformer_population_stats (bool const setting)
	Use conformer population data to weight sampling. Default TRUE. More...

void	set_root_prob_sampling (bool root_prob_sampling)
	Set the LCM to use probabilities for the ASN (or other residue) linkage. Default False. More...

void	set_defaults ()
	Set everything to default values, including linkage pairs. More...

bool	conformer_found () const
	Boolean for if the restype-dependant conformer was found at apply. Resets at successive applies. 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...

bool	reinitialize_for_new_input () const override
	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...

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

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

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...

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

This code changes all of the dihedrals of a particular glycosidic linkage based on database info, esentially sampling carbohydrate dihedral conformers of two residues. Randomly samples on any set selector at each apply or (default) samples a linkage conformer for each residue set.

The linkage conformers are carbohydrate residue type and (and linkage oxygen) dependant ie MAN-MAN If data is not known here, by default we sample from restype-independant data. If there are multiple conformers for a given linkage, will randomly select from them.

3 Main Conformer Sampling Strategies:

Constructor & Destructor Documentation

protocols::carbohydrates::LinkageConformerMover::LinkageConformerMover ( )

Default constructor.

References set_defaults().

protocols::carbohydrates::LinkageConformerMover::LinkageConformerMover ( core::select::residue_selector::ResidueSelectorCOP selector )

Constructor with pair of residues in linkage we will build the conformer for.

References set_defaults(), and set_residue_selector().

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

References omega_sampler_mover_, phi_sampler_mover_, psi_sampler_mover_, and selector_.

protocols::carbohydrates::LinkageConformerMover::~LinkageConformerMover ( )

overridedefault

Member Function Documentation

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

overridevirtual

Main Method.

Implements protocols::moves::Mover.

References conformer_found_, core::pose::Pose::glycan_tree_set(), idealize_torsions_, core::chemical::carbohydrates::CarbohydrateInfoManager::linkages_from_pair(), protocols::moves::MS_FAIL, protocols::moves::MS_SUCCESS, omega_sampler_mover_, core::chemical::carbohydrates::CarbohydrateInfoManager::pair_has_linkage_statistics(), phi_sampler_mover_, psi_sampler_mover_, protocols::moves::Mover::reset_status(), core::pose::Pose::residue_type(), core::scoring::rg, root_prob_sampling_, sample_protein_linkage_, core::select::residue_selector::selection_positions(), selector_, core::pose::carbohydrates::set_dihedrals_from_linkage_conformer_data(), protocols::moves::Mover::set_last_move_status(), protocols::TR(), use_conformer_population_stats_, use_gaussian_sampling_, and use_sugar_bb_data_if_needed_.

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

overridevirtual

required in the context of the parser/scripting scheme

Reimplemented from protocols::moves::Mover.

bool protocols::carbohydrates::LinkageConformerMover::conformer_found ( ) const

Boolean for if the restype-dependant conformer was found at apply. Resets at successive applies.

References conformer_found_.

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

overridevirtual

required in the context of the parser/scripting scheme

Reimplemented from protocols::moves::Mover.

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

overridevirtual

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

Implements protocols::moves::Mover.

References mover_name().

Referenced by provide_citation_info().

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

static

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

void protocols::carbohydrates::LinkageConformerMover::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 idealize_torsions_, core::select::residue_selector::parse_residue_selector(), root_prob_sampling_, sample_protein_linkage_, selector_, set_root_prob_sampling(), use_conformer_population_stats_, use_gaussian_sampling_, and use_sugar_bb_data_if_needed_.

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

overridevirtual

Provide the citation.

Reimplemented from protocols::moves::Mover.

References get_name(), omega_sampler_mover_, phi_sampler_mover_, psi_sampler_mover_, and selector_.

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

static

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

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

bool protocols::carbohydrates::LinkageConformerMover::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.

bool protocols::carbohydrates::LinkageConformerMover::reinitialize_for_new_input ( ) const

inlineoverridevirtual

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).

Movers default to not regenerating

Reimplemented from protocols::moves::Mover.

void protocols::carbohydrates::LinkageConformerMover::set_defaults ( )

Set everything to default values, including linkage pairs.

References conformer_found_, idealize_torsions_, core::id::omega_dihedral, omega_sampler_mover_, core::id::phi_dihedral, phi_sampler_mover_, core::id::psi_dihedral, psi_sampler_mover_, root_prob_sampling_, sample_protein_linkage_, use_conformer_population_stats_, use_gaussian_sampling_, and use_sugar_bb_data_if_needed_.

Referenced by LinkageConformerMover().

void protocols::carbohydrates::LinkageConformerMover::set_idealize_torsions ( bool idealize_torsions )

Idealize the torsion angles instead of sampling from SD. Default FALSE.

References idealize_torsions_.

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

Set the Selector. Each apply will randomly sample Selector. If the conformer is not found, will set move status to false. Will optimize the linkage between the residue and the parent residue.

References selector_.

Referenced by LinkageConformerMover().

void protocols::carbohydrates::LinkageConformerMover::set_root_prob_sampling ( bool root_prob_sampling )

Set the LCM to use probabilities for the ASN (or other residue) linkage. Default False.

References root_prob_sampling_.

Referenced by parse_my_tag().

void protocols::carbohydrates::LinkageConformerMover::set_single_resnum	(	core::pose::Pose const &	pose,
		core::Size	resnum
	)

Set a single resnum to sample on instead of a movemap.

References selector_, and core::pose::Pose::total_residue().

void protocols::carbohydrates::LinkageConformerMover::set_use_conformer_population_stats ( bool const setting )

inline

Use conformer population data to weight sampling. Default TRUE.

References use_conformer_population_stats_.

void protocols::carbohydrates::LinkageConformerMover::set_use_gaussian_sampling ( bool prob_sd_sample )

Set whether if we are sampling uniformly within 1 SD or by sampling on the full gaussian directly. Default FALSE.

References use_gaussian_sampling_.

void protocols::carbohydrates::LinkageConformerMover::set_use_sugar_bb_data_if_needed ( bool use_sugar_bb )

Use phi/psi data if restype-dependant conformer data unavailable. Will set phi/psi to lowest energy values if idealize is true. Default FALSE.

References use_sugar_bb_data_if_needed_.

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

overridevirtual

Outputs details about the Mover, including current settings.

Ideally, a child Mover should call Mover.show() and add additional information particular to that Mover.

Reimplemented from protocols::moves::Mover.

References protocols::moves::Mover::show().

Referenced by protocols::carbohydrates::operator<<().

Member Data Documentation

bool protocols::carbohydrates::LinkageConformerMover::conformer_found_

private

Referenced by apply(), conformer_found(), and set_defaults().

bool protocols::carbohydrates::LinkageConformerMover::idealize_torsions_

private

Referenced by apply(), parse_my_tag(), set_defaults(), and set_idealize_torsions().

simple_moves::BBDihedralSamplerMoverOP protocols::carbohydrates::LinkageConformerMover::omega_sampler_mover_

private

Referenced by apply(), LinkageConformerMover(), provide_citation_info(), and set_defaults().

simple_moves::BBDihedralSamplerMoverOP protocols::carbohydrates::LinkageConformerMover::phi_sampler_mover_

private

Referenced by apply(), LinkageConformerMover(), provide_citation_info(), and set_defaults().

simple_moves::BBDihedralSamplerMoverOP protocols::carbohydrates::LinkageConformerMover::psi_sampler_mover_

private

Referenced by apply(), LinkageConformerMover(), provide_citation_info(), and set_defaults().

bool protocols::carbohydrates::LinkageConformerMover::random_sampler_ = false

private

bool protocols::carbohydrates::LinkageConformerMover::root_prob_sampling_ = false

private

Referenced by apply(), parse_my_tag(), set_defaults(), and set_root_prob_sampling().

bool protocols::carbohydrates::LinkageConformerMover::sample_protein_linkage_

private

Referenced by apply(), parse_my_tag(), and set_defaults().

core::select::residue_selector::ResidueSelectorCOP protocols::carbohydrates::LinkageConformerMover::selector_ = nullptr

private

Referenced by apply(), LinkageConformerMover(), parse_my_tag(), provide_citation_info(), set_residue_selector(), and set_single_resnum().

bool protocols::carbohydrates::LinkageConformerMover::use_conformer_population_stats_

private

Referenced by apply(), parse_my_tag(), set_defaults(), and set_use_conformer_population_stats().

bool protocols::carbohydrates::LinkageConformerMover::use_gaussian_sampling_

private

Referenced by apply(), parse_my_tag(), set_defaults(), and set_use_gaussian_sampling().

bool protocols::carbohydrates::LinkageConformerMover::use_sugar_bb_data_if_needed_

private

Referenced by apply(), parse_my_tag(), set_defaults(), and set_use_sugar_bb_data_if_needed().

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

src/protocols/carbohydrates/LinkageConformerMover.hh
src/protocols/carbohydrates/LinkageConformerMover.cc

Private Attributes
bool	use_sugar_bb_data_if_needed_

bool	idealize_torsions_

bool	conformer_found_

bool	use_gaussian_sampling_

bool	sample_protein_linkage_

bool	use_conformer_population_stats_

bool	random_sampler_ = false

simple_moves::BBDihedralSamplerMoverOP	phi_sampler_mover_

simple_moves::BBDihedralSamplerMoverOP	psi_sampler_mover_

simple_moves::BBDihedralSamplerMoverOP	omega_sampler_mover_

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

bool	root_prob_sampling_ = false

Public Member Functions

Static Public Member Functions

Private Attributes

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation