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protocols::helical_bundle::FitSimpleHelix Class Reference

#include <FitSimpleHelix.hh>

Inheritance diagram for protocols::helical_bundle::FitSimpleHelix:
Inheritance graph
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Public Member Functions

 FitSimpleHelix ()
 Creator for FitSimpleHelix mover. More...
 
 ~FitSimpleHelix () override
 Destructor for FitSimpleHelix mover. More...
 
protocols::moves::MoverOP clone () const override
 Clone operator to create a pointer to a fresh FitSimpleHelix object that copies this one. More...
 
protocols::moves::MoverOP fresh_instance () const override
 Fresh_instance operator to create a pointer to a fresh FitSimpleHelix object that does NOT copy this one. More...
 
void apply (core::pose::Pose &pose) override
 Actually apply the mover to the pose. More...
 
void parse_my_tag (utility::tag::TagCOP tag, basic::datacache::DataMap &data) override
 parse XML (specifically in the context of the parser/Rosetta_scripting scheme) More...
 
void set_initial_guesses (core::Real const &r1_initial, core::Real const &omega1_initial, core::Real const &dz1_initial)
 
void set_range (core::Size const start, core::Size const end)
 
void set_min_type (std::string const &min_type)
 Set the minimization type (e.g. dfpmin, linmin, etc.) More...
 
void set_min_tolerance (core::Real const &min_tol_in)
 Set the minimizer tolerance (defaults to 1E-7, the default for many other protocols). More...
 
void set_reference_atom (std::string const &ref_atom_in)
 Set the mainchain atom that will be fit first, and used as the reference for other mainchain atoms. More...
 
void set_reference_residue (core::Size const ref_res_in)
 Set the residue in the repeating unit (1, 2, 3, etc.) that contains the reference atom. More...
 
core::Size reference_residue () const
 Get the reference residue index in the repeating unit. More...
 
void set_residues_per_repeat (core::Size const count_in)
 Set the number of residues per repeating unit in the helix. More...
 
core::Size residues_per_repeat () const
 Get the number of residues per repeating unit in the helix. More...
 
void get_crick_parameters (utility::vector1< core::Real > &r1_out, core::Real &omega1_out, core::Real &z1_out, utility::vector1< core::Real > &delta_omega1_out, utility::vector1< core::Real > &delta_z1_out) const
 Function to retrieve the final values of the helical parameters, post-fit. More...
 
void set_r1_guesses (utility::vector1< core::Real > const &r1_guesses_in)
 Load in guesses for the radii (optional during fitter setup). More...
 
void set_delta_omega1_guesses (utility::vector1< core::Real > const &delta_omega1_guesses_in)
 Load in guesses for the delta_omega1 values (optional during fitter setup). More...
 
void set_delta_z1_guesses (utility::vector1< core::Real > const &delta_z1_guesses_in)
 Load in guesses for the delta_z1 values (optional during fitter setup). More...
 
void set_rms_offset (core::Real const &rms_offset_in)
 Set the small float used to offset certain values in the RMS calculation to avoid zero determinants. 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 void show (std::ostream &output=std::cout) const
 Outputs details about the Mover, including current settings. 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::Real r1_initial_
 Initial guess for r1. More...
 
core::Real omega1_initial_
 Initial guess for omega1. More...
 
core::Real dz1_initial_
 Initial guess for dz1, the rise per residue. More...
 
core::Size start_index_
 Index of first residue in helix. More...
 
core::Size end_index_
 Index of last residue in helix. More...
 
std::string min_type_
 The type of minimization that will be used. More...
 
core::Real min_tolerance_
 The minimizer tolerance. More...
 
std::string reference_atom_
 The mainchain torsion atom to be used as the reference atom. More...
 
core::Size reference_residue_
 If the number of residues in the repeating unit is greater than one, which residue is the one that contains the reference atom? More...
 
core::Size residues_per_repeat_
 How many residues are there in the repeating unit? More...
 
utility::vector1< core::Realr1_vals_output_
 Output radii values (one for each atom fitted by the fitter). More...
 
core::Real omega1_val_output_
 Output omega1 value (turn per residue, shared by all atoms fitted by the fitter). More...
 
core::Real z1_val_output_
 Output z1 value (rise per residue, shared by all atoms fitted by the fitter). More...
 
utility::vector1< core::Realdelta_omega1_vals_output_
 Output delta_omega1 values (radial offset, one for each atom fitted by the fitter). More...
 
utility::vector1< core::Realdelta_z1_vals_output_
 Output delta_z1 values (z offset, one for each atom fitted by the fitter). More...
 
utility::vector1< core::Realr1_guesses_
 Vector of guesses for radii. More...
 
utility::vector1< core::Realdelta_omega1_guesses_
 Vector of guesses for offset around z-axis. More...
 
utility::vector1< core::Realdelta_z1_guesses_
 Vector of guesses for offset along z-axis. More...
 
core::Real rms_offset_
 A small float used to offset certain values in the RMS calculation to avoid zero determinants. 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...
 

Constructor & Destructor Documentation

protocols::helical_bundle::FitSimpleHelix::FitSimpleHelix ( )

Creator for FitSimpleHelix mover.

protocols::helical_bundle::FitSimpleHelix::~FitSimpleHelix ( )
overridedefault

Destructor for FitSimpleHelix mover.

Member Function Documentation

void protocols::helical_bundle::FitSimpleHelix::apply ( core::pose::Pose pose)
overridevirtual
protocols::moves::MoverOP protocols::helical_bundle::FitSimpleHelix::clone ( ) const
overridevirtual

Clone operator to create a pointer to a fresh FitSimpleHelix object that copies this one.

Reimplemented from protocols::moves::Mover.

protocols::moves::MoverOP protocols::helical_bundle::FitSimpleHelix::fresh_instance ( ) const
overridevirtual

Fresh_instance operator to create a pointer to a fresh FitSimpleHelix object that does NOT copy this one.

Reimplemented from protocols::moves::Mover.

void protocols::helical_bundle::FitSimpleHelix::get_crick_parameters ( utility::vector1< core::Real > &  r1_out,
core::Real omega1_out,
core::Real z1_out,
utility::vector1< core::Real > &  delta_omega1_out,
utility::vector1< core::Real > &  delta_z1_out 
) const

Function to retrieve the final values of the helical parameters, post-fit.

Returns the name of this mover ("FitSimpleHelix").

Call this function after the "apply" function, and pass it containers for the data to be retrieved.

Function to retrieve the final values of the helical parameters, post-fit.

Call this function after the "apply" function, and pass it containers for the data to be retrieved.

References delta_omega1_vals_output_, delta_z1_vals_output_, omega1_val_output_, r1_vals_output_, and z1_val_output_.

std::string protocols::helical_bundle::FitSimpleHelix::get_name ( ) const
overridevirtual

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

Implements protocols::moves::Mover.

References mover_name().

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

parse XML (specifically in the context of the parser/Rosetta_scripting scheme)

Reimplemented from protocols::moves::Mover.

References set_initial_guesses(), set_min_tolerance(), set_min_type(), set_range(), set_reference_atom(), set_reference_residue(), and set_residues_per_repeat().

void protocols::helical_bundle::FitSimpleHelix::provide_xml_schema ( utility::tag::XMLSchemaDefinition &  xsd)
static
core::Size protocols::helical_bundle::FitSimpleHelix::reference_residue ( ) const
inline

Get the reference residue index in the repeating unit.

References reference_residue_.

Referenced by apply().

core::Size protocols::helical_bundle::FitSimpleHelix::residues_per_repeat ( ) const
inline

Get the number of residues per repeating unit in the helix.

References residues_per_repeat_.

Referenced by apply().

void protocols::helical_bundle::FitSimpleHelix::set_delta_omega1_guesses ( utility::vector1< core::Real > const &  delta_omega1_guesses_in)
inline

Load in guesses for the delta_omega1 values (optional during fitter setup).

References delta_omega1_guesses_.

void protocols::helical_bundle::FitSimpleHelix::set_delta_z1_guesses ( utility::vector1< core::Real > const &  delta_z1_guesses_in)
inline

Load in guesses for the delta_z1 values (optional during fitter setup).

References delta_z1_guesses_.

void protocols::helical_bundle::FitSimpleHelix::set_initial_guesses ( core::Real const &  r1_initial,
core::Real const &  omega1_initial,
core::Real const &  dz1_initial 
)
inline

References dz1_initial_, omega1_initial_, and r1_initial_.

Referenced by parse_my_tag().

void protocols::helical_bundle::FitSimpleHelix::set_min_tolerance ( core::Real const &  min_tol_in)
inline

Set the minimizer tolerance (defaults to 1E-7, the default for many other protocols).

References min_tolerance_.

Referenced by parse_my_tag().

void protocols::helical_bundle::FitSimpleHelix::set_min_type ( std::string const &  min_type)
inline

Set the minimization type (e.g. dfpmin, linmin, etc.)

Defaults to dfpmin if not set.

References min_type_.

Referenced by parse_my_tag().

void protocols::helical_bundle::FitSimpleHelix::set_r1_guesses ( utility::vector1< core::Real > const &  r1_guesses_in)
inline

Load in guesses for the radii (optional during fitter setup).

References r1_guesses_.

void protocols::helical_bundle::FitSimpleHelix::set_range ( core::Size const  start,
core::Size const  end 
)
inline
void protocols::helical_bundle::FitSimpleHelix::set_reference_atom ( std::string const &  ref_atom_in)
inline

Set the mainchain atom that will be fit first, and used as the reference for other mainchain atoms.

If not set, this defaults to "CA".

References reference_atom_.

Referenced by parse_my_tag().

void protocols::helical_bundle::FitSimpleHelix::set_reference_residue ( core::Size const  ref_res_in)
inline

Set the residue in the repeating unit (1, 2, 3, etc.) that contains the reference atom.

If not set, this defaults to 1.

References reference_residue_.

Referenced by parse_my_tag().

void protocols::helical_bundle::FitSimpleHelix::set_residues_per_repeat ( core::Size const  count_in)
inline

Set the number of residues per repeating unit in the helix.

If not set, this defaults to 1.

References residues_per_repeat_.

Referenced by parse_my_tag().

void protocols::helical_bundle::FitSimpleHelix::set_rms_offset ( core::Real const &  rms_offset_in)
inline

Set the small float used to offset certain values in the RMS calculation to avoid zero determinants.

If fits produce bad geometry, this may need to be increased slightly.

References rms_offset_.

Member Data Documentation

utility::vector1< core::Real > protocols::helical_bundle::FitSimpleHelix::delta_omega1_guesses_
private

Vector of guesses for offset around z-axis.

Referenced by apply(), and set_delta_omega1_guesses().

utility::vector1< core::Real > protocols::helical_bundle::FitSimpleHelix::delta_omega1_vals_output_
private

Output delta_omega1 values (radial offset, one for each atom fitted by the fitter).

Referenced by apply(), and get_crick_parameters().

utility::vector1< core::Real > protocols::helical_bundle::FitSimpleHelix::delta_z1_guesses_
private

Vector of guesses for offset along z-axis.

Referenced by apply(), and set_delta_z1_guesses().

utility::vector1< core::Real > protocols::helical_bundle::FitSimpleHelix::delta_z1_vals_output_
private

Output delta_z1 values (z offset, one for each atom fitted by the fitter).

Referenced by apply(), and get_crick_parameters().

core::Real protocols::helical_bundle::FitSimpleHelix::dz1_initial_
private

Initial guess for dz1, the rise per residue.

Referenced by apply(), and set_initial_guesses().

core::Size protocols::helical_bundle::FitSimpleHelix::end_index_
private

Index of last residue in helix.

Referenced by apply(), and set_range().

core::Real protocols::helical_bundle::FitSimpleHelix::min_tolerance_
private

The minimizer tolerance.

Referenced by apply(), and set_min_tolerance().

std::string protocols::helical_bundle::FitSimpleHelix::min_type_
private

The type of minimization that will be used.

Referenced by apply(), and set_min_type().

core::Real protocols::helical_bundle::FitSimpleHelix::omega1_initial_
private

Initial guess for omega1.

Referenced by apply(), and set_initial_guesses().

core::Real protocols::helical_bundle::FitSimpleHelix::omega1_val_output_
private

Output omega1 value (turn per residue, shared by all atoms fitted by the fitter).

Referenced by apply(), and get_crick_parameters().

utility::vector1< core::Real > protocols::helical_bundle::FitSimpleHelix::r1_guesses_
private

Vector of guesses for radii.

Referenced by apply(), and set_r1_guesses().

core::Real protocols::helical_bundle::FitSimpleHelix::r1_initial_
private

Initial guess for r1.

Referenced by apply(), and set_initial_guesses().

utility::vector1< core::Real > protocols::helical_bundle::FitSimpleHelix::r1_vals_output_
private

Output radii values (one for each atom fitted by the fitter).

Referenced by apply(), and get_crick_parameters().

std::string protocols::helical_bundle::FitSimpleHelix::reference_atom_
private

The mainchain torsion atom to be used as the reference atom.

The fitter will first fit r1, omega1, and dz1 (the radius, turn per residue, and rise per residue) of the reference atom. For all other mainchain atoms, the fitter will then solve for r1' and the omega and z offsets, keeping omega and dz1 constant across all mainchain atoms.

Referenced by apply(), and set_reference_atom().

core::Size protocols::helical_bundle::FitSimpleHelix::reference_residue_
private

If the number of residues in the repeating unit is greater than one, which residue is the one that contains the reference atom?

Defaults to 1.

Referenced by reference_residue(), and set_reference_residue().

core::Size protocols::helical_bundle::FitSimpleHelix::residues_per_repeat_
private

How many residues are there in the repeating unit?

Defaults to 1.

Referenced by residues_per_repeat(), and set_residues_per_repeat().

core::Real protocols::helical_bundle::FitSimpleHelix::rms_offset_
private

A small float used to offset certain values in the RMS calculation to avoid zero determinants.

If fits produce bad geometry, this may need to be increased slightly.

Referenced by apply(), and set_rms_offset().

core::Size protocols::helical_bundle::FitSimpleHelix::start_index_
private

Index of first residue in helix.

Referenced by apply(), and set_range().

core::Real protocols::helical_bundle::FitSimpleHelix::z1_val_output_
private

Output z1 value (rise per residue, shared by all atoms fitted by the fitter).

Referenced by apply(), and get_crick_parameters().


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