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protocols::nmr::pre::PREMover Class Reference

#include <PREMover.hh>

Inheritance diagram for protocols::nmr::pre::PREMover:
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Public Types

typedef core::Real Real
 
typedef core::Size Size
 
typedef
core::scoring::nmr::pre::PREData 
PREData
 
typedef
core::scoring::nmr::pre::PREDataOP 
PREDataOP
 
typedef
core::scoring::nmr::pre::PREDataOP 
PREDataCOP
 
typedef
core::scoring::ScoreFunctionOP 
ScoreFunctionOP
 
typedef
core::scoring::ScoreFunctionCOP 
ScoreFunctionCOP
 
typedef core::pose::Pose Pose
 
typedef protocols::moves::MoverOP MoverOP
 
typedef std::map< std::string,
std::pair< std::string,
core::Real > > 
SpinlabelHistogramMap
 
typedef utility::vector1
< PREDistanceRecord
PREDistances
 
typedef std::map< core::Size,
PREDistances
SpinlabelToPREDistances
 
typedef
utility::fixedsizearray1< Real, 8 > 
Vec8
 
- 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
 

Public Member Functions

 PREMover ()
 Default constructor. More...
 
 PREMover (std::string const &pre_data_file, Pose const &pose)
 Construct PREMover from PRE data input file. More...
 
 PREMover (PREMover const &other)
 Copy constructor. More...
 
PREMoveroperator= (PREMover const &rhs)
 Copy assignment. More...
 
 ~PREMover () override
 destructor More...
 
std::string get_name () const override
 Get the name of this mover. More...
 
MoverOP clone () const override
 Make a deep copy of this mover. More...
 
MoverOP fresh_instance () const override
 Create a fresh instance of this mover. More...
 
void apply (Pose &pose) override
 Calculate CB-CB distances from PRE rates and append them as atom pair distance constraints to the pose. More...
 
void show (std::ostream &TR) const override
 Outputs details about the Mover, including current settings. More...
 
void parse_my_tag (utility::tag::TagCOP tag, basic::datacache::DataMap &datamap) override
 Parse tags of XML script. More...
 
PREDataCOP get_pre_data ()
 
std::string const & get_pre_data_file ()
 
ScoreFunctionCOP get_scorefunction () const
 
bool weighted_average () const
 
bool minimize_w_pre_csts () const
 
void set_pre_data (PREDataCOP pre_data)
 
void set_scorefunction (ScoreFunctionCOP sfxn)
 
void set_weighted_average (bool av)
 
void set_minimize_w_pre_csts (bool min)
 
void add_histogram_file (std::string const &spinlabel_name, std::string const &histogram_file, Real bin_size=0.5)
 
- 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 void provide_citation_info (basic::citation_manager::CitationCollectionList &) const
 Provide citations to the passed CitationCollectionList Subclasses should add the info for themselves and any other classes they use. More...
 

Static Public Member Functions

static std::string mover_name ()
 
static void provide_xml_schema (utility::tag::XMLSchemaDefinition &xsd)
 Create XML schema definition for PREMover. More...
 
- 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

Real R2_to_dist_dd_curie (Vec8 const &params, Real const R2)
 Calculate distance from R2 relaxation rate. More...
 
Real R1_to_dist_dd_curie (Vec8 const &params, Real const R1)
 Calculate distance from R1 relaxation rate. More...
 
void pre_data_to_distances (core::scoring::nmr::pre::PREData const &pre_data, SpinlabelToPREDistances &all_sl_distances)
 Calculate distances from relaxation rates and map them to their respective spinlabel and protein residue(s) More...
 

Private Attributes

SpinlabelHistogramMap histogram_files_
 Map of histogram files for very spinlabel type that is used in pre_data_. The histogram is used for instantiation of a SplineFunc potential for conversion of the measured PRE distance (e.g. for HN) into a CB-CB atom pair constraint. More...
 
PREDataCOP pre_data_
 collection of all PRE datasets for multiple spinlabel sites More...
 
std::string pre_data_file_
 The file to read the PRE data from at apply time. More...
 
ScoreFunctionCOP sfxn_
 scorefunction object More...
 
bool weighted_average_
 use PRESingleSet weights to calculate an average distance in case that the same PRE distance was measured multiple times (e.g. at different field strengths) for the same spinlabel site More...
 
bool minimize_
 Do one round of minimization of input pose after PRE distances constraints are added to the pose. More...
 

Additional Inherited Members

- 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...
 

Member Typedef Documentation

typedef std::map< std::string, std::pair< std::string, core::Real > > protocols::nmr::pre::PREMover::SpinlabelHistogramMap
typedef utility::fixedsizearray1< Real, 8 > protocols::nmr::pre::PREMover::Vec8

Constructor & Destructor Documentation

protocols::nmr::pre::PREMover::PREMover ( )

Default constructor.

References core::scoring::get_score_function(), and sfxn_.

Referenced by clone().

protocols::nmr::pre::PREMover::PREMover ( std::string const &  pre_data_file,
Pose const &  pose 
)

Construct PREMover from PRE data input file.

References histogram_files_, pre_data_, and protocols::nmr::pre::TR().

protocols::nmr::pre::PREMover::PREMover ( PREMover const &  other)
default

Copy constructor.

protocols::nmr::pre::PREMover::~PREMover ( )
override

destructor

Member Function Documentation

void protocols::nmr::pre::PREMover::add_histogram_file ( std::string const &  spinlabel_name,
std::string const &  histogram_file,
Real  bin_size = 0.5 
)

References histogram_files_.

Referenced by parse_my_tag().

void protocols::nmr::pre::PREMover::apply ( Pose pose)
overridevirtual
protocols::moves::MoverOP protocols::nmr::pre::PREMover::clone ( ) const
overridevirtual

Make a deep copy of this mover.

Reimplemented from protocols::moves::Mover.

References PREMover().

protocols::moves::MoverOP protocols::nmr::pre::PREMover::fresh_instance ( ) const
overridevirtual

Create a fresh instance of this mover.

Reimplemented from protocols::moves::Mover.

std::string protocols::nmr::pre::PREMover::get_name ( ) const
overridevirtual

Get the name of this mover.

Implements protocols::moves::Mover.

References mover_name().

PREDataCOP protocols::nmr::pre::PREMover::get_pre_data ( )
inline

Getter and Setters

Can be null

References pre_data_.

std::string const& protocols::nmr::pre::PREMover::get_pre_data_file ( )
inline

References pre_data_file_.

ScoreFunctionCOP protocols::nmr::pre::PREMover::get_scorefunction ( ) const
inline

References sfxn_.

bool protocols::nmr::pre::PREMover::minimize_w_pre_csts ( ) const
inline

References minimize_.

std::string protocols::nmr::pre::PREMover::mover_name ( )
static
PREMover & protocols::nmr::pre::PREMover::operator= ( PREMover const &  rhs)
default

Copy assignment.

void protocols::nmr::pre::PREMover::parse_my_tag ( utility::tag::TagCOP  tag,
basic::datacache::DataMap &  datamap 
)
overridevirtual
void protocols::nmr::pre::PREMover::pre_data_to_distances ( core::scoring::nmr::pre::PREData const &  pre_data,
SpinlabelToPREDistances all_sl_distances 
)
private
void protocols::nmr::pre::PREMover::provide_xml_schema ( utility::tag::XMLSchemaDefinition &  xsd)
static
core::Real protocols::nmr::pre::PREMover::R1_to_dist_dd_curie ( Vec8 const &  params,
Real const  R1 
)
private

Calculate distance from R1 relaxation rate.

Considers dipolar and Curie relaxation params[1] = gamma_I: gyromagnetic ratio of the nuclear spin (must be provided in rad/(s*T), dimension is 10^6) params[2] = gJ: electron Lande factor params[3] = S: total spin quantum number params[4] = omega_I: nuclear spin resonance frequency (must be provided in rad/s, dimension is 10^6) params[5] = tau_c: total correlation time (must be provided in s, typical dimension is 10^-9) params[6] = tau_r: rotational correlation time (must be provided in s, typical dimension is 10^-9) params[7] = B0: magnetic field strength (in Tesla) params[8] = T: temperature (in K) R1: R1 relaxation rate (in Hz)

Referenced by pre_data_to_distances().

core::Real protocols::nmr::pre::PREMover::R2_to_dist_dd_curie ( Vec8 const &  params,
Real const  R2 
)
private

Calculate distance from R2 relaxation rate.

Considers dipolar and Curie relaxation params[1] = gamma_I: gyromagnetic ratio of the nuclear spin (must be provided in rad/(s*T), dimension is 10^6) params[2] = gJ: electron Lande factor params[3] = S: total spin quantum number params[4] = omega_I: nuclear spin resonance frequency (must be provided in rad/s, dimension is 10^6) params[5] = tau_c: total correlation time (must be provided in s, typical dimension is 10^-9) params[6] = tau_r: rotational correlation time (must be provided in s, typical dimension is 10^-9) params[7] = B0: magnetic field strength (in Tesla) params[8] = T: temperature (in K) R2: R2 relaxation rate (in Hz)

Referenced by pre_data_to_distances().

void protocols::nmr::pre::PREMover::set_minimize_w_pre_csts ( bool  min)
inline
void protocols::nmr::pre::PREMover::set_pre_data ( PREDataCOP  pre_data)
inline

References pre_data_.

void protocols::nmr::pre::PREMover::set_scorefunction ( ScoreFunctionCOP  sfxn)
inline

References sfxn_.

void protocols::nmr::pre::PREMover::set_weighted_average ( bool  av)
inline

References weighted_average_.

void protocols::nmr::pre::PREMover::show ( std::ostream &  output) 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 histogram_files_, pre_data_, and pre_data_file_.

bool protocols::nmr::pre::PREMover::weighted_average ( ) const
inline

References weighted_average_.

Member Data Documentation

SpinlabelHistogramMap protocols::nmr::pre::PREMover::histogram_files_
private

Map of histogram files for very spinlabel type that is used in pre_data_. The histogram is used for instantiation of a SplineFunc potential for conversion of the measured PRE distance (e.g. for HN) into a CB-CB atom pair constraint.

Referenced by add_histogram_file(), apply(), PREMover(), and show().

bool protocols::nmr::pre::PREMover::minimize_
private

Do one round of minimization of input pose after PRE distances constraints are added to the pose.

Referenced by apply(), minimize_w_pre_csts(), parse_my_tag(), and set_minimize_w_pre_csts().

PREDataCOP protocols::nmr::pre::PREMover::pre_data_
private

collection of all PRE datasets for multiple spinlabel sites

Referenced by apply(), get_pre_data(), PREMover(), set_pre_data(), and show().

std::string protocols::nmr::pre::PREMover::pre_data_file_
private

The file to read the PRE data from at apply time.

Referenced by apply(), get_pre_data_file(), parse_my_tag(), and show().

ScoreFunctionCOP protocols::nmr::pre::PREMover::sfxn_
private

scorefunction object

Referenced by apply(), get_scorefunction(), parse_my_tag(), PREMover(), and set_scorefunction().

bool protocols::nmr::pre::PREMover::weighted_average_
private

use PRESingleSet weights to calculate an average distance in case that the same PRE distance was measured multiple times (e.g. at different field strengths) for the same spinlabel site

Referenced by parse_my_tag(), pre_data_to_distances(), set_weighted_average(), and weighted_average().


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