protocol to score local density-fit More...
#include <DensityZscores.hh>
Public Member Functions | |
| DensityZscores () | |
| Constructors ///. More... | |
| ~DensityZscores () override | |
| Destructor (important for properly forward-declaring smart-pointer members) More... | |
| core::Real | calc_avg_residue_bfac (core::Size const resi, core::pose::Pose const &pose) const |
| Mover Methods ///. More... | |
| core::Real | calc_avg_nbrhood_bfac (core::pose::Pose const &pose, core::Vector const x) const |
| get the average bfactor for a neighborhood More... | |
| utility::vector1< core::Real > | get_win1_denscc () const |
| utility::vector1< core::Real > | get_win3_denscc () const |
| utility::vector1< core::Real > | get_win1_dens_zscore () const |
| utility::vector1< core::Real > | get_win3_dens_zscore () const |
| utility::vector1< core::Real > | get_nbrhood_bfacs () const |
| utility::vector1< core::Real > | get_res_bfacs () const |
| void | apply (core::pose::Pose &pose) override |
| Apply the mover. 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 | provide_citation_info (basic::citation_manager::CitationCollectionList &citations) const override |
| This mover is unpublished. It returns Gabriella Reggiano as its author. 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 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... | |
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 const | NBRHD_DIST_ = 8.0 |
| core::Size const | LG_WIN_SIZE_ = 3 |
| core::Size const | SM_WIN_SIZE_ = 1 |
| utility::vector1< core::Real > | win1_denscc_ |
| utility::vector1< core::Real > | win3_denscc_ |
| utility::vector1< core::Real > | win1_dens_zscore_ |
| utility::vector1< core::Real > | win3_dens_zscore_ |
| utility::vector1< core::Real > | nbrhood_bfacs_ |
| utility::vector1< core::Real > | res_bfacs_ |
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
protocol to score local density-fit
Constructor & Destructor Documentation
◆ DensityZscores()
| protocols::electron_density::DensityZscores::DensityZscores | ( | ) |
Constructors ///.
Default constructor
◆ ~DensityZscores()
|
override |
Destructor (important for properly forward-declaring smart-pointer members)
Member Function Documentation
◆ apply()
|
overridevirtual |
Apply the mover.
Implements protocols::moves::Mover.
References calc_avg_nbrhood_bfac(), calc_avg_residue_bfac(), core::scoring::elec_dens_window, core::scoring::DensityZscoresStatsSetup::eval_zscore_by_resn_bfactor(), core::scoring::fa_rep, core::scoring::electron_density::getDensityMap(), core::pose::Pose::is_fullatom(), core::conformation::Residue::is_protein(), LG_WIN_SIZE_, core::scoring::electron_density::ElectronDensity::matchRes(), core::conformation::Residue::name3(), core::conformation::Residue::nbr_atom_xyz(), nbrhood_bfacs_, res_bfacs_, core::pose::Pose::residue(), core::scoring::electron_density::ElectronDensity::setScoreWindowContext(), core::scoring::electron_density::ElectronDensity::setWindow(), core::pose::Pose::size(), SM_WIN_SIZE_, core::scoring::vdw, win1_dens_zscore_, win1_denscc_, win3_dens_zscore_, and win3_denscc_.
◆ calc_avg_nbrhood_bfac()
| core::Real protocols::electron_density::DensityZscores::calc_avg_nbrhood_bfac | ( | core::pose::Pose const & | pose, |
| core::Vector const | x | ||
| ) | const |
get the average bfactor for a neighborhood
References core::conformation::Residue::atom_name(), core::conformation::Residue::atom_type(), core::chemical::AtomType::is_virtual(), core::conformation::Residue::is_virtual_residue(), core::conformation::Residue::nbr_atom_xyz(), NBRHD_DIST_, core::pose::Pose::pdb_info(), core::pose::Pose::residue(), and core::pose::Pose::total_residue().
Referenced by apply().
◆ calc_avg_residue_bfac()
| core::Real protocols::electron_density::DensityZscores::calc_avg_residue_bfac | ( | core::Size const | resi, |
| core::pose::Pose const & | pose | ||
| ) | const |
Mover Methods ///.
get the average bfactor for heavy atoms
References core::conformation::Residue::atom_name(), core::conformation::Residue::atom_type(), core::chemical::AtomType::is_virtual(), core::pose::Pose::pdb_info(), and core::pose::Pose::residue().
Referenced by apply().
◆ clone()
|
overridevirtual |
required in the context of the parser/scripting scheme
Reimplemented from protocols::moves::Mover.
◆ fresh_instance()
|
overridevirtual |
required in the context of the parser/scripting scheme
Reimplemented from protocols::moves::Mover.
◆ get_name()
|
overridevirtual |
Each derived class must specify its name. The class name.
Implements protocols::moves::Mover.
References mover_name().
◆ get_nbrhood_bfacs()
|
inline |
References nbrhood_bfacs_.
◆ get_res_bfacs()
|
inline |
References res_bfacs_.
◆ get_win1_dens_zscore()
|
inline |
References win1_dens_zscore_.
◆ get_win1_denscc()
|
inline |
References win1_denscc_.
◆ get_win3_dens_zscore()
|
inline |
References win3_dens_zscore_.
◆ get_win3_denscc()
|
inline |
References win3_denscc_.
◆ mover_name()
|
static |
Referenced by get_name(), protocols::electron_density::DensityZscoresCreator::keyname(), and provide_xml_schema().
◆ parse_my_tag()
|
overridevirtual |
Rosetta Scripts Support ///.
parse XML tag (to use this Mover in Rosetta Scripts)
Reimplemented from protocols::moves::Mover.
◆ provide_citation_info()
|
overridevirtual |
This mover is unpublished. It returns Gabriella Reggiano as its author.
Reimplemented from protocols::moves::Mover.
◆ provide_xml_schema()
|
static |
References mover_name(), and protocols::moves::xsd_type_definition_w_attributes().
Referenced by protocols::electron_density::DensityZscoresCreator::provide_xml_schema().
◆ show()
|
overridevirtual |
Show the contents of the Mover.
Reimplemented from protocols::moves::Mover.
References protocols::moves::Mover::show().
Referenced by protocols::electron_density::operator<<().
Member Data Documentation
◆ LG_WIN_SIZE_
|
private |
Referenced by apply().
◆ NBRHD_DIST_
|
private |
Referenced by calc_avg_nbrhood_bfac().
◆ nbrhood_bfacs_
|
private |
Referenced by apply(), and get_nbrhood_bfacs().
◆ res_bfacs_
|
private |
Referenced by apply(), and get_res_bfacs().
◆ SM_WIN_SIZE_
|
private |
Referenced by apply().
◆ win1_dens_zscore_
|
private |
Referenced by apply(), and get_win1_dens_zscore().
◆ win1_denscc_
|
private |
Referenced by apply(), and get_win1_denscc().
◆ win3_dens_zscore_
|
private |
Referenced by apply(), and get_win3_dens_zscore().
◆ win3_denscc_
|
private |
Referenced by apply(), and get_win3_denscc().
The documentation for this class was generated from the following files:
- src/protocols/electron_density/DensityZscores.hh
- src/protocols/electron_density/DensityZscores.cc
