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Rosetta
2016.11
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#include <SecStructFinder.hh>
Public Member Functions | |
SecStructFinder () | |
SecStructFinder (std::string residue, Size min_length=5, Size max_length=5, Real bin_size=10, Real dissimilarity=10, Real dihedral_min=-180, Real dihedral_max=180, Real dump_threshold=-10000, std::string dihedral_pattern="A", std::string alpha_beta_pattern="A", bool min_everything=false, bool cart=false, bool constrain=false) | |
virtual | ~SecStructFinder () |
virtual void | apply (Pose &pose) |
virtual std::string | get_name () const |
Each derived class must specify its name. The class name. More... | |
protocols::moves::MoverOP | fresh_instance () const |
Generates a new Mover object freshly created with the default ctor. More... | |
protocols::moves::MoverOP | clone () const |
Return a clone of the Mover object. More... | |
void | parse_my_tag (utility::tag::TagCOP, basic::datacache::DataMap &, protocols::filters::Filters_map const &, protocols::moves::Movers_map const &, core::pose::Pose const &) |
Called by MoverFactory when constructing new Movers. Takes care of the specific mover's parsing. More... | |
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Mover () | |
virtual | ~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... | |
Mover (Mover const &other) | |
Mover & | operator= (Mover const &other) |
assignment operator More... | |
virtual core::Real | last_proposal_density_ratio () |
std::string const & | type () const |
void | set_type (std::string const &setting) |
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 | set_current_tag (std::string const &new_tag) |
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 |
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... | |
void | type (const std::string &type_in) |
std::string | get_type () const |
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... | |
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 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... | |
void | set_current_job (protocols::jobdist::BasicJobCOP job) |
jobdist::BasicJobCOP | get_current_job () const |
virtual void | show (std::ostream &output=std::cout) const |
Outputs details about the Mover, including current settings. More... | |
Private Member Functions | |
std::string | alpha_to_beta (std::string alpha) |
std::string | expand_pattern_to_fit (std::string pattern, Size length) |
bool | uniq_refers_to_beta (char uniq) |
void | initialize_rtype_vector (utility::vector1< core::chemical::ResidueType > &restypes) |
std::string | make_filename (Size number_dihedrals, utility::vector1< Real > dihedrals) |
bool | too_similar (Size i, Size j, utility::vector1< Real > dihedrals) |
void | show_current_dihedrals (Size number_dihedral_sets, utility::vector1< char > uniqs, utility::vector1< Real > dihedrals) |
Private Attributes | |
core::scoring::ScoreFunctionOP | score_fxn_ |
std::string | residue_ |
Size | min_length_ |
Size | max_length_ |
Real | bin_size_ |
Real | dump_threshold_ |
Real | dihedral_min_ |
Real | dihedral_max_ |
std::string | dihedral_pattern_ |
std::string | alpha_beta_pattern_ |
bool | min_everything_ |
bool | cart_ |
bool | constrain_ |
Real | dissimilarity_ |
Additional Inherited Members | |
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typedef utility::tag::TagCOP | TagCOP |
typedef core::pose::Pose | Pose |
typedef core::pose::PoseCOP | PoseCOP |
typedef protocols::filters::Filters_map | Filters_map |
typedef std::list< std::string > | Strings |
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static std::string | name () |
static void | register_options () |
Overload this static method if you access options within the mover. More... | |
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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... | |
protocols::ncbb::SecStructFinder::SecStructFinder | ( | ) |
References core::scoring::constraints::add_fa_constraints_from_cmdline_to_scorefxn(), core::scoring::get_score_function(), and score_fxn_.
Referenced by clone().
protocols::ncbb::SecStructFinder::SecStructFinder | ( | std::string | residue, |
Size | min_length = 5 , |
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Size | max_length = 5 , |
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Real | bin_size = 10 , |
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Real | dissimilarity = 10 , |
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Real | dihedral_min = -180 , |
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Real | dihedral_max = 180 , |
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Real | dump_threshold = -10000 , |
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std::string | dihedral_pattern = "A" , |
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std::string | alpha_beta_pattern = "A" , |
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bool | min_everything = false , |
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bool | cart = false , |
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bool | constrain = false |
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inlinevirtual |
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private |
Referenced by initialize_rtype_vector().
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Implements protocols::moves::Mover.
References alpha_beta_pattern_, core::pose::Pose::append_residue_by_bond(), core::pose::Pose::append_residue_by_jump(), core::id::BB, bin_size_, cart_, protocols::simple_moves::MinMover::cartesian(), constrain_, protocols::ncbb::count_uniq_char(), core::scoring::dihedral_constraint, dihedral_max_, dihedral_min_, dihedral_pattern_, core::pose::Pose::dump_scored_pdb(), dump_threshold_, protocols::abinitio::filename(), protocols::ncbb::get_number_dihedrals(), protocols::ncbb::give_dihedral_index(), initialize_rtype_vector(), core::chemical::ResidueType::is_beta_aa(), make_filename(), min_everything_, min_length_, core::pose::Pose::n_residue(), core::pose::Pose::phi(), core::pose::Pose::psi(), core::pose::Pose::residue(), core::pose::Pose::residue_type(), protocols::hybridization::score, score_fxn_, core::pose::Pose::set_omega(), core::pose::Pose::set_phi(), core::pose::Pose::set_psi(), core::pose::Pose::set_torsion(), show_current_dihedrals(), too_similar(), core::pose::Pose::torsion(), protocols::TR(), and core::conformation::Residue::type().
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virtual |
Return a clone of the Mover object.
clone is meant to return an OP'ed deep copy of this object. This really should be a pure virtual in the base class, but adding pure virtuals to Mover would massively disrupt the code. This default implementation crashes at runtime instead of compiletime if you try to call it. If this code is causing you problems, your Mover needs to override this function.
Reimplemented from protocols::moves::Mover.
References alpha_beta_pattern_, bin_size_, cart_, dihedral_max_, dihedral_min_, dihedral_pattern_, dissimilarity_, dump_threshold_, max_length_, min_everything_, min_length_, residue_, and SecStructFinder().
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private |
Referenced by parse_my_tag(), and SecStructFinder().
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inlinevirtual |
Generates a new Mover object freshly created with the default ctor.
fresh_instance is meant to return a new object of this class, created with the default constructor. This really should be a pure virtual in the base class, but adding pure virtuals to Mover would massively disrupt the code. This default implementation crashes at runtime instead of compiletime if you try to call it. If this code is causing you problems, your Mover needs to override this function. This is used by the August 08 job distributor.
Reimplemented from protocols::moves::Mover.
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inlinevirtual |
Each derived class must specify its name. The class name.
Implements protocols::moves::Mover.
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private |
References alpha_beta_pattern_, alpha_to_beta(), core::chemical::FA_STANDARD, min_length_, protocols::moves::Mover::name(), and residue_.
Referenced by apply().
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References dihedral_pattern_, protocols::abinitio::filename(), min_length_, and residue_.
Referenced by apply().
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virtual |
Called by MoverFactory when constructing new Movers. Takes care of the specific mover's parsing.
Some movers need not be parsed, so we shouldn't stop executions. This, however, calls attention to the lack of this method, which could be due to something as silly as a wrong parameters definition.
Reimplemented from protocols::moves::Mover.
References alpha_beta_pattern_, bin_size_, cart_, dihedral_pattern_, dissimilarity_, dump_threshold_, expand_pattern_to_fit(), max_length_, min_everything_, min_length_, and residue_.
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References alpha_beta_pattern_, dihedral_pattern_, protocols::ncbb::give_dihedral_index(), protocols::TR(), and uniq_refers_to_beta().
Referenced by apply().
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References alpha_beta_pattern_, and dissimilarity_.
Referenced by apply().
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References alpha_beta_pattern_, and dihedral_pattern_.
Referenced by show_current_dihedrals().
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Referenced by apply(), clone(), initialize_rtype_vector(), parse_my_tag(), SecStructFinder(), show_current_dihedrals(), too_similar(), and uniq_refers_to_beta().
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Referenced by apply(), clone(), and parse_my_tag().
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Referenced by apply(), clone(), and parse_my_tag().
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Referenced by apply(), clone(), and SecStructFinder().
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Referenced by apply(), clone(), and SecStructFinder().
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Referenced by apply(), clone(), make_filename(), parse_my_tag(), SecStructFinder(), show_current_dihedrals(), and uniq_refers_to_beta().
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Referenced by clone(), parse_my_tag(), and too_similar().
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Referenced by apply(), clone(), and parse_my_tag().
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Referenced by clone(), parse_my_tag(), and SecStructFinder().
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Referenced by apply(), clone(), and parse_my_tag().
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Referenced by apply(), clone(), initialize_rtype_vector(), make_filename(), parse_my_tag(), and SecStructFinder().
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Referenced by clone(), initialize_rtype_vector(), make_filename(), and parse_my_tag().
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Referenced by apply(), and SecStructFinder().