#include <FitSimpleHelix.hh>
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 Strings & | info () |
| 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) |
| 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::Real > | r1_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::Real > | delta_omega1_vals_output_ |
| Output delta_omega1 values (radial offset, one for each atom fitted by the fitter). More... | |
| utility::vector1< core::Real > | delta_z1_vals_output_ |
| Output delta_z1 values (z offset, one for each atom fitted by the fitter). More... | |
| utility::vector1< core::Real > | r1_guesses_ |
| Vector of guesses for radii. More... | |
| utility::vector1< core::Real > | delta_omega1_guesses_ |
| Vector of guesses for offset around z-axis. More... | |
| utility::vector1< core::Real > | delta_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
◆ FitSimpleHelix()
| protocols::helical_bundle::FitSimpleHelix::FitSimpleHelix | ( | ) |
Creator for FitSimpleHelix mover.
◆ ~FitSimpleHelix()
|
overridedefault |
Destructor for FitSimpleHelix mover.
Member Function Documentation
◆ apply()
|
overridevirtual |
Actually apply the mover to the pose.
At the end of this function, two things will have happened: –The pose will be realigned to the ideal helix. –The fitted helical parameters will have been stored in internal variables for the mover, and can be retrieved with a call to get_crick_parameters().
Implements protocols::moves::Mover.
References core::conformation::Residue::atom_index(), core::chemical::ResidueType::atom_name(), core::id::AtomID::BOGUS_ATOM_ID(), delta_omega1_guesses_, delta_omega1_vals_output_, delta_z1_guesses_, delta_z1_vals_output_, dz1_initial_, end_index_, core::pose::initialize_atomid_map(), core::chemical::ResidueType::mainchain_atom(), min_tolerance_, min_type_, core::conformation::Residue::n_mainchain_atoms(), core::conformation::Residue::natoms(), omega1_initial_, omega1_val_output_, r1_guesses_, r1_initial_, r1_vals_output_, reference_atom_, reference_residue(), core::pose::Pose::residue(), core::pose::Pose::residue_type(), residues_per_repeat(), rms_offset_, core::optimization::Minimizer::run(), core::pose::Pose::set_xyz(), core::pose::Pose::size(), start_index_, core::scoring::superimpose_pose(), protocols::hybridization::t, protocols::helical_bundle::TR(), core::pose::Pose::xyz(), protocols::kinmatch::xyz(), and z1_val_output_.
◆ clone()
|
overridevirtual |
Clone operator to create a pointer to a fresh FitSimpleHelix object that copies this one.
Reimplemented from protocols::moves::Mover.
◆ fresh_instance()
|
overridevirtual |
Fresh_instance operator to create a pointer to a fresh FitSimpleHelix object that does NOT copy this one.
Reimplemented from protocols::moves::Mover.
◆ get_crick_parameters()
| 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_.
◆ get_name()
|
overridevirtual |
Each derived class must specify its name. The class name.
Implements protocols::moves::Mover.
References mover_name().
◆ mover_name()
|
static |
Referenced by get_name(), protocols::helical_bundle::FitSimpleHelixCreator::keyname(), and provide_xml_schema().
◆ parse_my_tag()
|
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().
◆ provide_xml_schema()
|
static |
References mover_name(), and protocols::moves::xsd_type_definition_w_attributes().
Referenced by protocols::helical_bundle::FitSimpleHelixCreator::provide_xml_schema().
◆ reference_residue()
|
inline |
Get the reference residue index in the repeating unit.
References reference_residue_.
Referenced by apply().
◆ residues_per_repeat()
|
inline |
Get the number of residues per repeating unit in the helix.
References residues_per_repeat_.
Referenced by apply().
◆ set_delta_omega1_guesses()
|
inline |
Load in guesses for the delta_omega1 values (optional during fitter setup).
References delta_omega1_guesses_.
◆ set_delta_z1_guesses()
|
inline |
Load in guesses for the delta_z1 values (optional during fitter setup).
References delta_z1_guesses_.
◆ set_initial_guesses()
|
inline |
References dz1_initial_, omega1_initial_, and r1_initial_.
Referenced by parse_my_tag().
◆ set_min_tolerance()
|
inline |
Set the minimizer tolerance (defaults to 1E-7, the default for many other protocols).
References min_tolerance_.
Referenced by parse_my_tag().
◆ set_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().
◆ set_r1_guesses()
|
inline |
Load in guesses for the radii (optional during fitter setup).
References r1_guesses_.
◆ set_range()
|
inline |
References core::sequence::end, end_index_, protocols::loops::start, and start_index_.
Referenced by parse_my_tag().
◆ set_reference_atom()
|
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().
◆ set_reference_residue()
|
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().
◆ set_residues_per_repeat()
|
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().
◆ set_rms_offset()
|
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
◆ delta_omega1_guesses_
|
private |
Vector of guesses for offset around z-axis.
Referenced by apply(), and set_delta_omega1_guesses().
◆ 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().
◆ delta_z1_guesses_
|
private |
Vector of guesses for offset along z-axis.
Referenced by apply(), and set_delta_z1_guesses().
◆ 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().
◆ dz1_initial_
|
private |
Initial guess for dz1, the rise per residue.
Referenced by apply(), and set_initial_guesses().
◆ end_index_
|
private |
Index of last residue in helix.
Referenced by apply(), and set_range().
◆ min_tolerance_
|
private |
The minimizer tolerance.
Referenced by apply(), and set_min_tolerance().
◆ min_type_
|
private |
The type of minimization that will be used.
Referenced by apply(), and set_min_type().
◆ omega1_initial_
|
private |
Initial guess for omega1.
Referenced by apply(), and set_initial_guesses().
◆ 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().
◆ r1_guesses_
|
private |
Vector of guesses for radii.
Referenced by apply(), and set_r1_guesses().
◆ r1_initial_
|
private |
Initial guess for r1.
Referenced by apply(), and set_initial_guesses().
◆ r1_vals_output_
|
private |
Output radii values (one for each atom fitted by the fitter).
Referenced by apply(), and get_crick_parameters().
◆ 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().
◆ 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().
◆ 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().
◆ 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().
◆ start_index_
|
private |
Index of first residue in helix.
Referenced by apply(), and set_range().
◆ 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:
- src/protocols/helical_bundle/FitSimpleHelix.hh
- src/protocols/helical_bundle/FitSimpleHelix.cc
