Rosetta  2020.37
 All Classes Namespaces Files Functions Variables Typedefs Enumerations Enumerator Friends Macros Pages
Public Member Functions | Static Public Member Functions | Private Attributes | List of all members
protocols::carbohydrates::LinkageConformerMover Class Reference

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:
Inheritance graph
[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...
 
bool mover_provides_citation_info () const override
 Does this mover provide information about how to cite it? More...
 
utility::vector1
< basic::citation_manager::CitationCollectionCOP > 
provide_citation_info () const override
 Provide the citation. More...
 
utility::vector1
< basic::citation_manager::UnpublishedModuleInfoCOP > 
provide_authorship_info_for_unpublished () const override
 Provide a list of authors and their e-mail addresses, as strings. 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 Stringsinfo ()
 non-const accessor More...
 
virtual Strings const & info () const
 const accessor More...
 
virtual bool mover_is_unpublished () const
 Does this mover indicate that it is unpublished (and, by extension, that the author should be included in publications resulting from it)? 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 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
 

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

Member Function Documentation

void protocols::carbohydrates::LinkageConformerMover::apply ( core::pose::Pose )
overridevirtual
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
bool protocols::carbohydrates::LinkageConformerMover::mover_provides_citation_info ( ) const
overridevirtual

Does this mover provide information about how to cite it?

Returns true – this mover does.

Author
Vikram K. Mulligan (vmull.nosp@m.igan.nosp@m.@flat.nosp@m.iron.nosp@m.insti.nosp@m.tute.nosp@m..org)

Reimplemented from protocols::moves::Mover.

void protocols::carbohydrates::LinkageConformerMover::parse_my_tag ( utility::tag::TagCOP  tag,
basic::datacache::DataMap &  data 
)
overridevirtual
utility::vector1< basic::citation_manager::UnpublishedModuleInfoCOP > protocols::carbohydrates::LinkageConformerMover::provide_authorship_info_for_unpublished ( ) const
overridevirtual

Provide a list of authors and their e-mail addresses, as strings.

Returns
Empty list by default, since this mover is published. Can provide information about modules that this mover invokes.
Author
Vikram K. Mulligan (vmull.nosp@m.igan.nosp@m.@flat.nosp@m.iron.nosp@m.insti.nosp@m.tute.nosp@m..org)

Reimplemented from protocols::moves::Mover.

References omega_sampler_mover_, phi_sampler_mover_, psi_sampler_mover_, and selector_.

utility::vector1< basic::citation_manager::CitationCollectionCOP > protocols::carbohydrates::LinkageConformerMover::provide_citation_info ( ) const
overridevirtual

Provide the citation.

Returns
A vector of citation collections. This mover was published in Labonte et al. (2017).

Also provides citations for modules invoked by this mover.

Author
Vikram K. Mulligan (vmull.nosp@m.igan.nosp@m.@flat.nosp@m.iron.nosp@m.insti.nosp@m.tute.nosp@m..org)

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
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 ( )
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
bool protocols::carbohydrates::LinkageConformerMover::idealize_torsions_
private
simple_moves::BBDihedralSamplerMoverOP protocols::carbohydrates::LinkageConformerMover::omega_sampler_mover_
private
simple_moves::BBDihedralSamplerMoverOP protocols::carbohydrates::LinkageConformerMover::phi_sampler_mover_
private
simple_moves::BBDihedralSamplerMoverOP protocols::carbohydrates::LinkageConformerMover::psi_sampler_mover_
private
bool protocols::carbohydrates::LinkageConformerMover::random_sampler_ = false
private
bool protocols::carbohydrates::LinkageConformerMover::root_prob_sampling_ = false
private
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
bool protocols::carbohydrates::LinkageConformerMover::use_conformer_population_stats_
private
bool protocols::carbohydrates::LinkageConformerMover::use_gaussian_sampling_
private
bool protocols::carbohydrates::LinkageConformerMover::use_sugar_bb_data_if_needed_
private

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