Rosetta Protocols  2014.35
Public Member Functions | Private Attributes | List of all members
protocols::make_rot_lib::MakeRotLibMover Class Reference

#include <MakeRotLibMover.hh>

Public Member Functions

 MakeRotLibMover ()
 Default constructor. More...
 
virtual ~MakeRotLibMover ()
 
virtual void apply (core::pose::Pose &pose)
 
virtual std::string get_name () const
 Each derived class must specify its name. The class name. More...
 
void init_centroids (CentroidRotNumVecVec const &centroid_data, core::Size num_chi)
 Initializes centroid arrays based on data from the MRLOptionsData. More...
 
void init_rotamers (TorsionRangeVec const &chi_ranges, core::Size num_clusters, core::Real omg, core::Real phi, core::Real psi, core::Real eps)
 Initializes rotamer arrays based on data from the MRLOptionsData. More...
 
void minimize_rotamer (RotData &rd, core::pose::Pose &pose, MakeRotLibPolymerType polymer_type)
 
void minimize_all_rotamers (core::pose::Pose &pose, MakeRotLibPolymerType polymer_type)
 
void calc_all_dist ()
 
bool calc_rotamer_clusters ()
 Determins closest cluster centroid for all rotamers. More...
 
bool calc_centroids ()
 
void calc_final_rotamers ()
 
void calc_final_rotamer_probs ()
 
void calc_standard_deviations (core::pose::Pose &pose, MakeRotLibPolymerType polymer_type)
 
void make_two_fold_symetry_135_315 (RotDataVec &rdv, core::Size chi_num)
 brief Use to symetrize if the 2 rotamers are falling near 0 (360) and 90 (270) like the symetric chi2 of phenylalanine More...
 
void make_two_fold_symetry_0_180 (RotDataVec &rdv, core::Size chi_num)
 brief Use to symetrize if the 1 rotamer is falling near 90 (270) like the symetric chi1 of a n-aryl peptoid More...
 
void make_three_fold_symetry_90_210_330 (RotDataVec &rdv, core::Size chi_num)
 brief Use to symetrize if the 2 rotamers are falling near 0 and 60 like with a tert-butyl group More...
 
void print_rot_data (RotData &rd, std::ostream &os)
 
void print_rot_data_vec (RotDataVec &rdv, std::ostream &os)
 
core::Real print_avg_cluster_centroid_dist (std::ostream &os)
 
void print_dunbrack02_rotlib (core::Real omg, core::Real phi, core::Real psi, 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 ~Mover ()
 
virtual MoverSP create ()
 
virtual void apply (core::io::serialization::PipeMap &pmap)
 
virtual void parse_state (SerializableState const &state)
 
virtual void parse_def (utility::lua::LuaObject const &def, utility::lua::LuaObject const &score_fxns, utility::lua::LuaObject const &tasks, MoverCacheSP cache)
 
virtual void save_state (SerializableState &state)
 
 Mover (std::string const &type_name)
 sets the type for a mover; name_ has been removed (2010/05/14) More...
 
 Mover (Mover const &other)
 
Moveroperator= (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...
 
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)
 
virtual MoverOP clone () const
 Return a clone of the Mover object. More...
 
virtual void parse_my_tag (TagCOP tag, basic::datacache::DataMap &data, Filters_map const &filters, Movers_map const &movers, Pose const &pose)
 Called by MoverFactory when constructing new Movers. Takes care of the specific mover's parsing. More...
 
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 Stringsinfo ()
 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...
 
virtual MoverOP fresh_instance () const
 Generates a new Mover object freshly created with the default ctor. 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 Attributes

core::scoring::ScoreFunctionOP scrfxn_
 
RotDataVec centroids_
 
RotDataVec rotamers_
 
RotDataVec final_rotamers_
 

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
protocols::filters::Filters_map 
Filters_map
 
typedef std::list< std::stringStrings
 
- 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 ( )
virtual protocols::make_rot_lib::MakeRotLibMover::~MakeRotLibMover ( )
inlinevirtual

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 pose)
virtual
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_, and protocols::make_rot_lib::TR.

Referenced by apply().

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

References centroids_, final_rotamers_, num_clusters, 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 )

References numeric::nonnegative_principal_angle_degrees(), and numeric::principal_angle_degrees().

Referenced by calc_centroids().

void protocols::make_rot_lib::MakeRotLibMover::calc_standard_deviations ( core::pose::Pose pose,
MakeRotLibPolymerType  polymer_type 
)
virtual std::string protocols::make_rot_lib::MakeRotLibMover::get_name ( ) const
inlinevirtual

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 
)

Initializes centroid arrays based on data from the MRLOptionsData.

References angle, and centroids_.

Referenced by apply().

void protocols::make_rot_lib::MakeRotLibMover::init_rotamers ( TorsionRangeVec const &  chi_ranges,
core::Size  num_clusters,
core::Real  omg,
core::Real  phi,
core::Real  psi,
core::Real  eps 
)

Initializes rotamer arrays based on data from the MRLOptionsData.

References l, and rotamers_.

Referenced by apply().

void protocols::make_rot_lib::MakeRotLibMover::make_three_fold_symetry_90_210_330 ( RotDataVec rdv,
core::Size  chi_num 
)

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

References numeric::nonnegative_principal_angle_degrees().

Referenced by apply().

void protocols::make_rot_lib::MakeRotLibMover::make_two_fold_symetry_0_180 ( RotDataVec rdv,
core::Size  chi_num 
)

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

References numeric::nonnegative_principal_angle_degrees().

Referenced by apply().

void protocols::make_rot_lib::MakeRotLibMover::make_two_fold_symetry_135_315 ( RotDataVec rdv,
core::Size  chi_num 
)

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

References numeric::nonnegative_principal_angle_degrees().

Referenced by apply().

void protocols::make_rot_lib::MakeRotLibMover::minimize_all_rotamers ( core::pose::Pose pose,
MakeRotLibPolymerType  polymer_type 
)
void protocols::make_rot_lib::MakeRotLibMover::minimize_rotamer ( RotData rd,
core::pose::Pose pose,
MakeRotLibPolymerType  polymer_type 
)

References protocols::simple_moves::MinMover::apply(), chemical, core::pose::Pose::chi(), core::pose::Pose::energies(), fa_sol, protocols::make_rot_lib::RotData::get_eps(), protocols::make_rot_lib::RotData::get_inp_chi(), protocols::make_rot_lib::RotData::get_num_chi(), protocols::make_rot_lib::RotData::get_omg(), protocols::make_rot_lib::RotData::get_phi(), protocols::make_rot_lib::RotData::get_psi(), mm_lj_inter_atr, mm_lj_inter_rep, mm_lj_intra_atr, mm_lj_intra_rep, mm_twist, numeric::nonnegative_principal_angle_degrees(), protocols::make_rot_lib::PEPTIDE, protocols::make_rot_lib::PEPTOID, core::scoring::Energies::residue_total_energies(), scoring, scrfxn_, core::kinematics::MoveMap::set(), core::pose::Pose::set_chi(), core::kinematics::MoveMap::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_solvation(), core::pose::Pose::set_torsion(), protocols::make_rot_lib::RotData::set_twist(), core::pose::Pose::torsion(), core::scoring::Energies::total_energy(), protocols::make_rot_lib::TR, and utility_exit_with_message.

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_dunbrack02_rotlib ( core::Real  omg,
core::Real  phi,
core::Real  psi,
core::Real  eps,
MakeRotLibPolymerType  polymer_type,
std::ostream &  os 
)
void protocols::make_rot_lib::MakeRotLibMover::print_rot_data ( RotData rd,
std::ostream &  os 
)
void protocols::make_rot_lib::MakeRotLibMover::print_rot_data_vec ( RotDataVec rdv,
std::ostream &  os 
)

References print_rot_data().

Referenced by apply().

Member Data Documentation

RotDataVec protocols::make_rot_lib::MakeRotLibMover::centroids_
private
RotDataVec protocols::make_rot_lib::MakeRotLibMover::final_rotamers_
private
RotDataVec protocols::make_rot_lib::MakeRotLibMover::rotamers_
private
core::scoring::ScoreFunctionOP protocols::make_rot_lib::MakeRotLibMover::scrfxn_
private

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