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protocols::farnesyl::SampleFarnesylMover Class Reference

Modifies a free cysteine residue with a branch of 3 DMA residues (the terpene monomer) to create farnesyl-cysteine. More...

#include <SampleFarnesylMover.hh>

Inheritance diagram for protocols::farnesyl::SampleFarnesylMover:
Inheritance graph
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Public Member Functions

 SampleFarnesylMover ()
 Constructors ///. More...
 
 SampleFarnesylMover (SampleFarnesylMover const &src)
 Copy constructor (not needed unless you need deep copies) More...
 
 ~SampleFarnesylMover () override
 Destructor (important for properly forward-declaring smart-pointer members) More...
 
void apply (core::pose::Pose &pose) override
 Mover Methods ///. More...
 
void sample_farnesyl (core::pose::Pose &pose, core::Size const cys_idx, core::Size const dma_one_idx, core::Size const dma_two_idx, core::Size const dma_three_idx)
 Mover Methods ///. More...
 
void show (std::ostream &output=std::cout) const override
 Show the contents of the Mover. 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_score_function (core::scoring::ScoreFunctionOP const &sfxn)
 
void set_enumerate (bool const enumerate)
 
- 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 Stringsinfo ()
 non-const accessor More...
 
virtual Strings const & info () const
 const accessor More...
 
virtual bool mover_provides_citation_info () const
 Does this mover provide information about how to cite it? More...
 
virtual utility::vector1
< basic::citation_manager::CitationCollectionCOP > 
provide_citation_info () const
 Provide the citation. 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...
 
virtual utility::vector1
< basic::citation_manager::UnpublishedModuleInfoCOP > 
provide_authorship_info_for_unpublished () const
 Provide a list of authors and their e-mail addresses, as strings. 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

core::scoring::ScoreFunctionOP sfxn_ = nullptr
 
bool enumerate_ = true
 

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

Modifies a free cysteine residue with a branch of 3 DMA residues (the terpene monomer) to create farnesyl-cysteine.

Constructor & Destructor Documentation

protocols::farnesyl::SampleFarnesylMover::SampleFarnesylMover ( )

Constructors ///.

Default constructor

protocols::farnesyl::SampleFarnesylMover::SampleFarnesylMover ( SampleFarnesylMover const &  src)

Copy constructor (not needed unless you need deep copies)

Copy constructor.

protocols::farnesyl::SampleFarnesylMover::~SampleFarnesylMover ( )
override

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

Member Function Documentation

void protocols::farnesyl::SampleFarnesylMover::apply ( core::pose::Pose pose)
overridevirtual

Mover Methods ///.

Apply the mover.

Apply the mover

Loop through every residue in the pose. If it's not cysteine – move on. if it has no conjugation – move on. If it doesn't have 3 pendant DMAs – move on. Then... you've found farnesyl cysteine; go to the sampling function.

Implements protocols::moves::Mover.

References core::chemical::ResidueTypeBase::aa(), core::chemical::aa_cys, core::chemical::ResidueType::atom_index(), core::conformation::Residue::connected_residue_at_resconn(), core::conformation::Residue::has_variant_type(), core::chemical::ResidueTypeBase::name3(), core::pose::Pose::residue(), core::chemical::ResidueType::residue_connection_id_for_atom(), core::pose::Pose::residue_type(), sample_farnesyl(), core::chemical::SC_BRANCH_POINT, core::pose::Pose::size(), and protocols::TR().

protocols::moves::MoverOP protocols::farnesyl::SampleFarnesylMover::clone ( ) const
overridevirtual

required in the context of the parser/scripting scheme

Reimplemented from protocols::moves::Mover.

protocols::moves::MoverOP protocols::farnesyl::SampleFarnesylMover::fresh_instance ( ) const
overridevirtual

required in the context of the parser/scripting scheme

Reimplemented from protocols::moves::Mover.

std::string protocols::farnesyl::SampleFarnesylMover::get_name ( ) const
overridevirtual

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

Implements protocols::moves::Mover.

References mover_name().

std::string protocols::farnesyl::SampleFarnesylMover::mover_name ( )
static
void protocols::farnesyl::SampleFarnesylMover::parse_my_tag ( utility::tag::TagCOP  tag,
basic::datacache::DataMap &  data 
)
overridevirtual

Rosetta Scripts Support ///.

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

Reimplemented from protocols::moves::Mover.

References core::scoring::parse_score_function(), set_enumerate(), and set_score_function().

void protocols::farnesyl::SampleFarnesylMover::provide_xml_schema ( utility::tag::XMLSchemaDefinition &  xsd)
static
void protocols::farnesyl::SampleFarnesylMover::sample_farnesyl ( core::pose::Pose pose,
core::Size const  cys_idx,
core::Size const  dma_one_idx,
core::Size const  dma_two_idx,
core::Size const  dma_three_idx 
)

Mover Methods ///.

Sample a particular farnesyl

Draw torsion combinations from a small library of options. Someone else (TM) can turn this rigorous (with explicit management of their relative probabilities, and perhaps registering these conformations in a useful way, and perhaps expanded and/or made dependent on CYS more explicitly. Or the InstallFarnesylMover could give you a custom library, optionally for this particular farnesyl. Plus, this should all be read in from a DB file). What a useful task list for someone else (TM)! Actually – the sampling process we've been using is pretty fast. I am going to actually use that every time. Why not! The fixed library subset paradigm can be used later. So now we do all this sampling and then take the best conformation forward.

References protocols::minimization_packing::MinMover::apply(), core::id::BB, core::chemical::rna::CHI, enumerate_, core::scoring::get_score_function(), protocols::hybridization::score, protocols::stepwise::sampler::StepWiseSamplerComb::set_random(), core::pose::Pose::set_torsion(), sfxn_, and protocols::TR().

Referenced by apply().

void protocols::farnesyl::SampleFarnesylMover::set_enumerate ( bool const  enumerate)
inline

References enumerate_.

Referenced by parse_my_tag().

void protocols::farnesyl::SampleFarnesylMover::set_score_function ( core::scoring::ScoreFunctionOP const &  sfxn)
inline

References sfxn_.

Referenced by parse_my_tag().

void protocols::farnesyl::SampleFarnesylMover::show ( std::ostream &  output = std::cout) const
overridevirtual

Show the contents of the Mover.

Reimplemented from protocols::moves::Mover.

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

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

Member Data Documentation

bool protocols::farnesyl::SampleFarnesylMover::enumerate_ = true
private

Referenced by sample_farnesyl(), and set_enumerate().

core::scoring::ScoreFunctionOP protocols::farnesyl::SampleFarnesylMover::sfxn_ = nullptr
private

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