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protocols::make_rot_lib::MakeRotLibMover Class Reference

#include <MakeRotLibMover.hh>

Inheritance diagram for protocols::make_rot_lib::MakeRotLibMover:
Inheritance graph
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Public Member Functions

 MakeRotLibMover (bool const write_log_file=true)
 Default constructor. More...
 
 ~MakeRotLibMover () override=default
 
void apply (core::pose::Pose &pose) override
 Main Method. More...
 
std::string get_name () const override
 Each derived class must specify its name. The class name. More...
 
void init_centroids (CentroidRotNumVecVec const &centroid_data, core::Size num_chi, bool semirotameric)
 Initializes centroid arrays based on data from the MRLOptionsData. More...
 
void init_rotamers (TorsionRangeVec const &chi_ranges, core::Size num_clusters, core::Real omg, utility::vector1< core::Real > bbs, utility::vector1< core::Size > bbids, core::Real eps, bool semirotameric)
 Initializes rotamer arrays based on data from the MRLOptionsData. More...
 
void minimize_rotamer (RotData &rd, core::pose::Pose &pose, utility::vector1< core::Real > bbs, utility::vector1< core::Size > bb_ids, MakeRotLibPolymerType polymer_type)
 
void minimize_all_rotamers (core::pose::Pose &pose, utility::vector1< core::Real > bbs, utility::vector1< core::Size > bb_ids, MakeRotLibPolymerType polymer_type)
 
void seed_centroids (bool semirotameric)
 For k-medoids, seed centroids to nearest element of rotamers_. More...
 
void calc_all_dist ()
 
bool calc_rotamer_clusters ()
 Determins closest cluster centroid for all rotamers. More...
 
bool calc_medoids ()
 
bool calc_centroids ()
 
bool bbs_appropriate_for_definitions (utility::vector1< core::Real > bbs)
 returns if you should print definitions from this file More...
 
void calc_final_rotamers ()
 
void calc_final_rotamer_probs ()
 
void calc_standard_deviations (core::pose::Pose &pose, utility::vector1< core::Real > bbs, utility::vector1< core::Size > bb_ids, MakeRotLibPolymerType polymer_type)
 
void make_two_fold_symmetry_135_315 (RotDataVec &rdv, core::Size chi_num)
 brief Use to symmetrize if the 2 rotamers are falling near 0 (360) and 90 (270) like the symmetric chi2 of phenylalanine More...
 
void make_two_fold_symmetry_0_180 (RotDataVec &rdv, core::Size chi_num)
 brief Use to symmetrize if the 1 rotamer is falling near 90 (270) like the symmetric chi1 of a n-aryl peptoid More...
 
void make_three_fold_symmetry_90_210_330 (RotDataVec &rdv, core::Size chi_num)
 brief Use to symmetrize if the 2 rotamers are falling near 0 and 60 like with a tert-butyl group More...
 
void print_rot_data (RotData &rd, utility::vector1< core::Size > bb_ids, std::ostream &os)
 
void print_rot_data_vec (RotDataVec &rdv, utility::vector1< core::Size > bb_ids, std::ostream &os)
 
core::Real print_avg_cluster_centroid_dist (std::ostream &os)
 
void print_dunbrack02_rotlib (core::Real omg, utility::vector1< core::Real > bbs, utility::vector1< core::Size > bbids, core::Real eps, MakeRotLibPolymerType polymer_type, std::ostream &os)
 
void print_definitions (std::ostream &os)
 
void print_dunbrack10_rotlib (core::Real omg, utility::vector1< core::Real > bbs, utility::vector1< core::Size > bbids, core::Real eps, MakeRotLibPolymerType polymer_type, std::ostream &os)
 
core::Real calc_dist (RotData &rd1, RotData &rd2)
 
core::Real angle_diff (core::Real a1, core::Real a2)
 
void calc_running_avg (core::Real angle_new, core::Real &angle_old, core::Size &count)
 calculates a runnig average. Tries to use the closest anglular value ( ie. the average of 350 degrees and 10 degrees should be 0 and not 180 )( ie. the average of 170 degrees and -170 degrees should be 180 and not 0 ) 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 MoverOP clone () const
 Return a clone of the Mover object. 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...
 
virtual MoverOP fresh_instance () const
 Generates a new Mover object freshly created with the default ctor. 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
 
virtual void parse_my_tag (TagCOP tag, basic::datacache::DataMap &data)
 Called by MoverFactory when constructing new Movers. Takes care of the specific mover's parsing. More...
 
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...
 

Private Attributes

core::scoring::ScoreFunctionOP scrfxn_
 
core::Real KbT_
 
RotDataVec centroids_
 
RotDataVec rotamers_
 
RotDataVec final_rotamers_
 
bool write_log_file_
 Are we writing a logfile for each application of the mover? Defaults to true, but can be disabled. 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
 
- 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...
 
- 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::make_rot_lib::MakeRotLibMover::MakeRotLibMover ( bool const  write_log_file = true)
protocols::make_rot_lib::MakeRotLibMover::~MakeRotLibMover ( )
overridedefault

Member Function Documentation

core::Real protocols::make_rot_lib::MakeRotLibMover::angle_diff ( core::Real  a1,
core::Real  a2 
)

Referenced by calc_dist().

void protocols::make_rot_lib::MakeRotLibMover::apply ( core::pose::Pose )
overridevirtual
bool protocols::make_rot_lib::MakeRotLibMover::bbs_appropriate_for_definitions ( utility::vector1< core::Real bbs)

returns if you should print definitions from this file

Referenced by apply().

void protocols::make_rot_lib::MakeRotLibMover::calc_all_dist ( )

References calc_dist(), centroids_, and rotamers_.

Referenced by apply().

bool protocols::make_rot_lib::MakeRotLibMover::calc_centroids ( )

References calc_running_avg(), centroids_, and rotamers_.

Referenced by apply().

core::Real protocols::make_rot_lib::MakeRotLibMover::calc_dist ( RotData rd1,
RotData rd2 
)
void protocols::make_rot_lib::MakeRotLibMover::calc_final_rotamer_probs ( )

References final_rotamers_, KbT_, and protocols::make_rot_lib::TR().

Referenced by apply().

void protocols::make_rot_lib::MakeRotLibMover::calc_final_rotamers ( )
bool protocols::make_rot_lib::MakeRotLibMover::calc_medoids ( )

References calc_dist(), centroids_, and rotamers_.

Referenced by apply().

bool protocols::make_rot_lib::MakeRotLibMover::calc_rotamer_clusters ( )

Determins closest cluster centroid for all rotamers.

References rotamers_.

Referenced by apply().

void protocols::make_rot_lib::MakeRotLibMover::calc_running_avg ( core::Real  angle_new,
core::Real angle_old,
core::Size count 
)

calculates a runnig average. Tries to use the closest anglular value ( ie. the average of 350 degrees and 10 degrees should be 0 and not 180 )( ie. the average of 170 degrees and -170 degrees should be 180 and not 0 )

Referenced by calc_centroids().

void protocols::make_rot_lib::MakeRotLibMover::calc_standard_deviations ( core::pose::Pose pose,
utility::vector1< core::Real bbs,
utility::vector1< core::Size bb_ids,
MakeRotLibPolymerType  polymer_type 
)
std::string protocols::make_rot_lib::MakeRotLibMover::get_name ( ) const
inlineoverridevirtual

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

Implements protocols::moves::Mover.

void protocols::make_rot_lib::MakeRotLibMover::init_centroids ( CentroidRotNumVecVec const &  centroid_data,
core::Size  num_chi,
bool  semirotameric 
)

Initializes centroid arrays based on data from the MRLOptionsData.

References centroids_.

Referenced by apply().

void protocols::make_rot_lib::MakeRotLibMover::init_rotamers ( TorsionRangeVec const &  chi_ranges,
core::Size  num_clusters,
core::Real  omg,
utility::vector1< core::Real bbs,
utility::vector1< core::Size bbids,
core::Real  eps,
bool  semirotameric 
)

Initializes rotamer arrays based on data from the MRLOptionsData.

References rotamers_.

Referenced by apply().

void protocols::make_rot_lib::MakeRotLibMover::make_three_fold_symmetry_90_210_330 ( RotDataVec rdv,
core::Size  chi_num 
)

brief Use to symmetrize if the 2 rotamers are falling near 0 and 60 like with a tert-butyl group

Referenced by apply().

void protocols::make_rot_lib::MakeRotLibMover::make_two_fold_symmetry_0_180 ( RotDataVec rdv,
core::Size  chi_num 
)

brief Use to symmetrize if the 1 rotamer is falling near 90 (270) like the symmetric chi1 of a n-aryl peptoid

Referenced by apply().

void protocols::make_rot_lib::MakeRotLibMover::make_two_fold_symmetry_135_315 ( RotDataVec rdv,
core::Size  chi_num 
)

brief Use to symmetrize if the 2 rotamers are falling near 0 (360) and 90 (270) like the symmetric chi2 of phenylalanine

Referenced by apply().

void protocols::make_rot_lib::MakeRotLibMover::minimize_all_rotamers ( core::pose::Pose pose,
utility::vector1< core::Real bbs,
utility::vector1< core::Size bb_ids,
MakeRotLibPolymerType  polymer_type 
)
void protocols::make_rot_lib::MakeRotLibMover::minimize_rotamer ( RotData rd,
core::pose::Pose pose,
utility::vector1< core::Real bbs,
utility::vector1< core::Size bb_ids,
MakeRotLibPolymerType  polymer_type 
)

References protocols::minimization_packing::MinMover::apply(), core::id::BB, core::pose::Pose::chi(), core::conformation::Residue::chi(), core::pose::Pose::conformation(), core::pose::Pose::energies(), core::scoring::fa_atr, core::scoring::fa_rep, core::scoring::fa_sol, protocols::make_rot_lib::RotData::get_bb(), protocols::make_rot_lib::RotData::get_eps(), protocols::make_rot_lib::RotData::get_inp_chi(), protocols::jd2::JobDistributor::get_instance(), protocols::make_rot_lib::RotData::get_min_chi(), protocols::make_rot_lib::RotData::get_num_chi(), protocols::make_rot_lib::RotData::get_omg(), protocols::make_rot_lib::RotData::get_semi_energy_dist(), protocols::make_rot_lib::RotData::get_semi_prob_dist(), protocols::make_rot_lib::RotData::get_semirotameric(), KbT_, core::conformation::Residue::mainchain_torsions(), core::scoring::mm_lj_intra_atr, core::scoring::mm_lj_intra_rep, core::scoring::mm_twist, protocols::make_rot_lib::PEPTIDE, protocols::make_rot_lib::PEPTOID, core::conformation::Conformation::residue(), core::pose::Pose::residue(), core::scoring::Energies::residue_total_energies(), protocols::make_rot_lib::RotData::resize_semi_vectors(), scrfxn_, core::pose::Pose::set_chi(), protocols::make_rot_lib::RotData::set_energy(), protocols::make_rot_lib::RotData::set_inter_atr(), protocols::make_rot_lib::RotData::set_inter_rep(), protocols::make_rot_lib::RotData::set_intra_atr(), protocols::make_rot_lib::RotData::set_intra_rep(), protocols::make_rot_lib::RotData::set_min_chi(), protocols::make_rot_lib::RotData::set_min_eps(), protocols::make_rot_lib::RotData::set_min_omg(), protocols::make_rot_lib::RotData::set_semi_energy_dist(), protocols::make_rot_lib::RotData::set_semi_prob_dist(), protocols::make_rot_lib::RotData::set_solvation(), core::pose::Pose::set_torsion(), protocols::make_rot_lib::RotData::set_twist(), core::pose::Pose::torsion(), core::scoring::Energies::total_energy(), and protocols::make_rot_lib::TR().

Referenced by calc_standard_deviations(), and minimize_all_rotamers().

core::Real protocols::make_rot_lib::MakeRotLibMover::print_avg_cluster_centroid_dist ( std::ostream &  os)

References centroids_, and rotamers_.

Referenced by apply().

void protocols::make_rot_lib::MakeRotLibMover::print_definitions ( std::ostream &  os)

References centroids_, final_rotamers_, and core::sequence::left.

Referenced by apply().

void protocols::make_rot_lib::MakeRotLibMover::print_dunbrack02_rotlib ( core::Real  omg,
utility::vector1< core::Real bbs,
utility::vector1< core::Size bbids,
core::Real  eps,
MakeRotLibPolymerType  polymer_type,
std::ostream &  os 
)
void protocols::make_rot_lib::MakeRotLibMover::print_dunbrack10_rotlib ( core::Real  omg,
utility::vector1< core::Real bbs,
utility::vector1< core::Size bbids,
core::Real  eps,
MakeRotLibPolymerType  polymer_type,
std::ostream &  os 
)
void protocols::make_rot_lib::MakeRotLibMover::print_rot_data ( RotData rd,
utility::vector1< core::Size bb_ids,
std::ostream &  os 
)
void protocols::make_rot_lib::MakeRotLibMover::print_rot_data_vec ( RotDataVec rdv,
utility::vector1< core::Size bb_ids,
std::ostream &  os 
)

References print_rot_data().

Referenced by apply().

void protocols::make_rot_lib::MakeRotLibMover::seed_centroids ( bool  semirotameric)

For k-medoids, seed centroids to nearest element of rotamers_.

References calc_dist(), centroids_, core::kinematics::distance(), and rotamers_.

Referenced by apply().

Member Data Documentation

RotDataVec protocols::make_rot_lib::MakeRotLibMover::centroids_
private
RotDataVec protocols::make_rot_lib::MakeRotLibMover::final_rotamers_
private
core::Real protocols::make_rot_lib::MakeRotLibMover::KbT_
private
RotDataVec protocols::make_rot_lib::MakeRotLibMover::rotamers_
private
core::scoring::ScoreFunctionOP protocols::make_rot_lib::MakeRotLibMover::scrfxn_
private
bool protocols::make_rot_lib::MakeRotLibMover::write_log_file_
private

Are we writing a logfile for each application of the mover? Defaults to true, but can be disabled.

Author
Vikram K. Mulligan (vmull.nosp@m.igan.nosp@m.@flat.nosp@m.iron.nosp@m.insti.nosp@m.tute.nosp@m..org)

Referenced by apply(), and MakeRotLibMover().


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