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protocols::ddg::ddGMover Class Reference

#include <ddGMover.hh>

Inheritance diagram for protocols::ddg::ddGMover:
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Public Member Functions

 ddGMover ()
 
 ddGMover (core::scoring::ScoreFunctionOP s, core::scoring::ScoreFunctionOP m, utility::vector1< core::chemical::AA > res_to_mutate)
 
virtual ~ddGMover ()
 
void neighbor_cutoff (double cutoff)
 
void restrict_to_nbrs (bool truefalse)
 
void score_function (core::scoring::ScoreFunctionOP s)
 
void set_minimization_score_function (core::scoring::ScoreFunctionOP s)
 
void num_iterations (int num)
 
void dump_pdbs (bool truefalse)
 
void debug_output (bool truefalse)
 
void is_interface_ddg (bool truefalse)
 
void wt_score_components (ObjexxFCL::FArray2D< double > wsc)
 
void wt_unbound_score_components (ObjexxFCL::FArray2D< double > wusc)
 
void mutant_score_components (ObjexxFCL::FArray2D< double > msc)
 
void residues_to_mutate (utility::vector1< core::chemical::AA > residues)
 
void set_min_cst (bool truefalse)
 
void set_mean (bool truefalse)
 
void set_min (bool truefalse)
 
void set_num_decoys_used_in_calculations (core::Real num_lowe_used)
 
core::Real neighbor_cutoff ()
 
bool restrict_to_nbrs ()
 
core::scoring::ScoreFunctionOP score_function ()
 
core::scoring::ScoreFunctionOP minimization_score_function ()
 
int num_iterations ()
 
bool is_interface_ddg ()
 
ObjexxFCL::FArray2D< double > wt_score_components ()
 
ObjexxFCL::FArray2D< double > wt_unbound_score_components ()
 
ObjexxFCL::FArray2D< double > mutant_score_components ()
 
utility::vector1
< core::chemical::AA
residues_to_mutate ()
 
utility::vector1< double > get_wt_min_score_components ()
 
utility::vector1< double > get_wt_averaged_score_components ()
 
utility::vector1< double > get_mutant_min_score_components ()
 
utility::vector1< double > get_mutant_averaged_score_components ()
 
utility::vector1< double > get_delta_energy_components ()
 
void get_scorefunction_header (core::scoring::ScoreFunctionOP sfxn, utility::vector1< std::string > &components)
 
std::string mutation_label (pose::Pose const &pose) const
 
double get_wt_averaged_totals ()
 
double get_wt_min_totals ()
 
double get_mutant_averaged_totals ()
 
double get_mutant_min_totals ()
 
double ddG ()
 
virtual void apply (core::pose::Pose &pose)
 
virtual std::string get_name () const
 Each derived class must specify its name. The class name. More...
 
bool is_wt_calc_complete ()
 
bool is_mutant_calc_complete ()
 
bool is_properly_initialized (pose::Pose &pose)
 
bool get_min_cst ()
 
bool use_mean ()
 
bool use_min ()
 
core::Real get_num_decoys_used_in_calculations ()
 
- 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
 
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
 clone has to be overridden only if clone invocation is expected. More...
 
virtual void parse_my_tag (TagPtr const tag, 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
 this function informs 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
 this function informs 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
 this is like clone(), except it generates a new mover object freshly created with the default ctor. This function should be pure virtual but that would disrupt the code base; MAKE SURE YOU DEFINE IT if you want to have your mover be a protocol handed to the job distributor (august 08 vintage). More...
 
void set_current_job (protocols::jobdist::BasicJobCOP job)
 
jobdist::BasicJobCOP get_current_job () const
 

Private Member Functions

utility::vector1< intfind_nbrs (core::pose::Pose &p, utility::vector1< int > &mutation_position, double radii)
 
void setup_packertask (core::pack::task::PackerTaskOP pt, core::pose::Pose &p)
 
bool is_complete (ObjexxFCL::FArray2D< double > to_check)
 
double sum (ddGs &scores_to_sum)
 
double average (utility::vector1< double > &scores_to_average)
 
int store_energies (ObjexxFCL::FArray2D< double > &two_d_e_arrays, core::scoring::ScoreFunction &s, core::pose::Pose &p, int next_index, int size_to_expect)
 
int average_score_components (ObjexxFCL::FArray2D< double > &scores_to_average, utility::vector1< double > &averaged_scores)
 
void calculate_interface_unbound_energy (core::pose::Pose &p, core::scoring::ScoreFunctionOP s, core::pack::task::PackerTaskOP pt)
 
void setup_rotamer_constraints (core::pose::Pose &p, core::scoring::ScoreFunction &s, utility::vector1< int > &mutation_position, bool all_but_mutation_site, utility::vector1< char > &constraints_at_pos)
 
void setup_repack_constraints (core::pose::Pose &pose, core::scoring::ScoreFunctionOP sfxn, bool all_but_mut_site, utility::vector1< char > &constraints_at_pos)
 sets up only rotamer constraints available during repacking More...
 
void setup_constraints (pose::Pose &pose, core::scoring::ScoreFunctionOP sfxn, float const cst_tol, bool all_but_mut_site, utility::vector1< char > &constraints_at_pos)
 
void minimize_with_constraints (pose::Pose &pose, core::scoring::ScoreFunctionOP s, core::pack::task::PackerTaskOP pt)
 
void print_verbose_ddgs (utility::vector1< pose::Pose > mut, utility::vector1< pose::Pose > wt, core::scoring::ScoreFunctionOP sfxn, bool mean, bool min, std::string filename)
 
void relax_wildtype_structure (core::pose::Pose &pose, protocols::scoring::Interface &protein_interface, std::string const &wt_traj, bool output_silent)
 APL's attempts at refactoring this code. More...
 
void setup_packer_task_for_mutations (core::pose::Pose const &pose, protocols::scoring::Interface const &protein_interface, utility::vector1< int > const &mutations, core::pack::task::PackerTaskOP packer_task)
 Initialize a packer task to reflect the residues that should be repacked based on the structure of the wildtype pose. More...
 
void initialize_task_level_behavior (core::pack::task::PackerTaskOP packer_task)
 
bool is_any_pdb_empty (core::pose::Pose const &pose, std::string const &mutant_traj, bool const output_silent) const
 
utility::vector1< boolneighborhood_of_mutations (core::pose::Pose const &pose, utility::vector1< int > const &mutations) const
 
void initialize_rotamer_behavior_for_residue_level_task (core::pack::task::ResidueLevelTask &rltask) const
 

Private Attributes

core::Real num_decoys_used_in_calculations_
 
bool mean_
 
bool min_
 
bool min_cst_
 
core::Real nbr_cutoff_
 
bool restrict_to_nbrhood_
 
bool interface_ddg_
 
core::scoring::ScoreFunctionOP scorefxn_
 
core::scoring::ScoreFunctionOP min_cst_sfxn_
 
core::scoring::ScoreFunctionOP min_cst_sfxn_no_cst_weight_
 minimize the score with this score function More...
 
core::scoring::constraints::ConstraintSetOP cst_set_
 report the score with this score function More...
 
core::scoring::constraints::ConstraintSetOP min_cst_set_wt_
 
utility::vector1< char > min_cst_wt_types_
 
core::scoring::constraints::ConstraintSetOP min_cst_set_mut_
 
utility::vector1< char > min_cst_mut_types_
 
core::scoring::constraints::ConstraintSetOP repack_cst_set_wt_
 
utility::vector1< char > repack_wt_types_
 
core::scoring::constraints::ConstraintSetOP repack_cst_set_mut_
 
utility::vector1< char > repack_mut_types_
 
utility::vector1
< core::chemical::AA
residues_to_mutate_
 
int num_iterations_
 
bool dmp_pdb_
 
bool dbg_output_
 
ObjexxFCL::FArray2D< double > wt_components_
 
ObjexxFCL::FArray2D< double > wt_unbound_components_
 
ObjexxFCL::FArray2D< double > mutant_components_
 
ObjexxFCL::FArray2D< double > mutant_unbound_components_
 
utility::vector1< pose::Posenatives_
 
utility::vector1< pose::Posemutants_
 

Additional Inherited Members

- Public Types inherited from protocols::moves::Mover
typedef utility::tag::TagPtr TagPtr
 
typedef core::pose::Pose Pose
 
typedef core::pose::PoseCOP PoseCOP
 
typedef
protocols::filters::Filters_map 
Filters_map
 
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. these options will end up in -help of your application if users of this mover call register_options. do this recursively! if you use movers within your mover, call their register_options in your register_options() method. 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::ddg::ddGMover::ddGMover ( )
protocols::ddg::ddGMover::ddGMover ( core::scoring::ScoreFunctionOP  s,
core::scoring::ScoreFunctionOP  m,
utility::vector1< core::chemical::AA res_to_mutate 
)
protocols::ddg::ddGMover::~ddGMover ( )
virtual

Member Function Documentation

void protocols::ddg::ddGMover::apply ( core::pose::Pose pose)
virtual
double protocols::ddg::ddGMover::average ( utility::vector1< double > &  scores_to_average)
private

References sum().

int protocols::ddg::ddGMover::average_score_components ( ObjexxFCL::FArray2D< double > &  scores_to_average,
utility::vector1< double > &  averaged_scores 
)
private
void protocols::ddg::ddGMover::calculate_interface_unbound_energy ( core::pose::Pose p,
core::scoring::ScoreFunctionOP  s,
core::pack::task::PackerTaskOP  pt 
)
private
double protocols::ddg::ddGMover::ddG ( )
void protocols::ddg::ddGMover::debug_output ( bool  truefalse)

References dbg_output_.

Referenced by protocols::ddG_main().

void protocols::ddg::ddGMover::dump_pdbs ( bool  truefalse)

References dmp_pdb_.

Referenced by protocols::ddG_main().

utility::vector1< int > protocols::ddg::ddGMover::find_nbrs ( core::pose::Pose p,
utility::vector1< int > &  mutation_position,
double  radii 
)
private
utility::vector1< double > protocols::ddg::ddGMover::get_delta_energy_components ( )
bool protocols::ddg::ddGMover::get_min_cst ( )

References min_cst_.

utility::vector1< double > protocols::ddg::ddGMover::get_mutant_averaged_score_components ( )
double protocols::ddg::ddGMover::get_mutant_averaged_totals ( )

References get_mutant_averaged_score_components(), and sum().

Referenced by ddG().

utility::vector1< double > protocols::ddg::ddGMover::get_mutant_min_score_components ( )
double protocols::ddg::ddGMover::get_mutant_min_totals ( )

References get_mutant_min_score_components(), and sum().

Referenced by apply(), and ddG().

std::string protocols::ddg::ddGMover::get_name ( ) const
virtual

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

Implements protocols::moves::Mover.

core::Real protocols::ddg::ddGMover::get_num_decoys_used_in_calculations ( )
void protocols::ddg::ddGMover::get_scorefunction_header ( core::scoring::ScoreFunctionOP  sfxn,
utility::vector1< std::string > &  components 
)
utility::vector1< double > protocols::ddg::ddGMover::get_wt_averaged_score_components ( )
double protocols::ddg::ddGMover::get_wt_averaged_totals ( )

References get_wt_averaged_score_components(), and sum().

Referenced by ddG().

utility::vector1< double > protocols::ddg::ddGMover::get_wt_min_score_components ( )
double protocols::ddg::ddGMover::get_wt_min_totals ( )

References get_wt_min_score_components(), and sum().

Referenced by apply(), and ddG().

void protocols::ddg::ddGMover::initialize_rotamer_behavior_for_residue_level_task ( core::pack::task::ResidueLevelTask rltask) const
private
void protocols::ddg::ddGMover::initialize_task_level_behavior ( core::pack::task::PackerTaskOP  packer_task)
private

Experimental: add extra options controlling how the packer behaves

Referenced by apply(), and relax_wildtype_structure().

bool protocols::ddg::ddGMover::is_any_pdb_empty ( core::pose::Pose const &  pose,
std::string const &  mutant_traj,
bool const  output_silent 
) const
private

determine if we need to do any work, or if we have checkpoints saving us from some work

References dmp_pdb_, mutation_label(), num_iterations_, core::io::silent::SilentFileData::read_file(), core::io::silent::SilentFileData::read_tags_fast(), and restrict_to_nbrhood_.

Referenced by apply().

bool protocols::ddg::ddGMover::is_complete ( ObjexxFCL::FArray2D< double >  to_check)
private
void protocols::ddg::ddGMover::is_interface_ddg ( bool  truefalse)

References interface_ddg_.

Referenced by protocols::ddG_main().

bool protocols::ddg::ddGMover::is_interface_ddg ( )

References interface_ddg_.

bool protocols::ddg::ddGMover::is_mutant_calc_complete ( )

References is_complete(), and mutant_components_.

Referenced by protocols::ddG_main().

bool protocols::ddg::ddGMover::is_properly_initialized ( pose::Pose pose)
bool protocols::ddg::ddGMover::is_wt_calc_complete ( )
core::scoring::ScoreFunctionOP protocols::ddg::ddGMover::minimization_score_function ( )

References min_cst_sfxn_.

void protocols::ddg::ddGMover::minimize_with_constraints ( pose::Pose pose,
core::scoring::ScoreFunctionOP  s,
core::pack::task::PackerTaskOP  pt 
)
private
void protocols::ddg::ddGMover::mutant_score_components ( ObjexxFCL::FArray2D< double >  msc)

References mutant_components_.

ObjexxFCL::FArray2D< double > protocols::ddg::ddGMover::mutant_score_components ( )

References mutant_components_.

std::string protocols::ddg::ddGMover::mutation_label ( pose::Pose const &  pose) const
void protocols::ddg::ddGMover::neighbor_cutoff ( double  cutoff)

References nbr_cutoff_.

Referenced by protocols::ddG_main().

Real protocols::ddg::ddGMover::neighbor_cutoff ( )

References nbr_cutoff_.

utility::vector1< bool > protocols::ddg::ddGMover::neighborhood_of_mutations ( core::pose::Pose const &  pose,
utility::vector1< int > const &  mutations 
) const
private
void protocols::ddg::ddGMover::num_iterations ( int  num)

References num_iterations_.

Referenced by protocols::ddG_main().

int protocols::ddg::ddGMover::num_iterations ( )

References num_iterations_.

void protocols::ddg::ddGMover::print_verbose_ddgs ( utility::vector1< pose::Pose mut,
utility::vector1< pose::Pose wt,
core::scoring::ScoreFunctionOP  sfxn,
bool  mean,
bool  min,
std::string  filename 
)
private
void protocols::ddg::ddGMover::relax_wildtype_structure ( core::pose::Pose pose,
protocols::scoring::Interface protein_interface,
std::string const &  wt_traj,
bool  output_silent 
)
private
void protocols::ddg::ddGMover::residues_to_mutate ( utility::vector1< core::chemical::AA residues)

References residues_to_mutate_.

Referenced by protocols::ddG_main().

utility::vector1< core::chemical::AA > protocols::ddg::ddGMover::residues_to_mutate ( )

References residues_to_mutate_.

void protocols::ddg::ddGMover::restrict_to_nbrs ( bool  truefalse)

References restrict_to_nbrhood_.

Referenced by protocols::ddG_main().

bool protocols::ddg::ddGMover::restrict_to_nbrs ( )

References restrict_to_nbrhood_.

void protocols::ddg::ddGMover::score_function ( core::scoring::ScoreFunctionOP  s)

References scorefxn_.

core::scoring::ScoreFunctionOP protocols::ddg::ddGMover::score_function ( )

References scorefxn_.

Referenced by minimize_with_constraints().

void protocols::ddg::ddGMover::set_mean ( bool  truefalse)

References mean_.

Referenced by protocols::ddG_main().

void protocols::ddg::ddGMover::set_min ( bool  truefalse)
void protocols::ddg::ddGMover::set_min_cst ( bool  truefalse)

References min_cst_.

Referenced by protocols::ddG_main().

void protocols::ddg::ddGMover::set_minimization_score_function ( core::scoring::ScoreFunctionOP  s)
void protocols::ddg::ddGMover::set_num_decoys_used_in_calculations ( core::Real  num_lowe_used)
void protocols::ddg::ddGMover::setup_constraints ( pose::Pose pose,
core::scoring::ScoreFunctionOP  sfxn,
float const  cst_tol,
bool  all_but_mut_site,
utility::vector1< char > &  constraints_at_pos 
)
private
void protocols::ddg::ddGMover::setup_packer_task_for_mutations ( core::pose::Pose const &  pose,
protocols::scoring::Interface const &  protein_interface,
utility::vector1< int > const &  mutations,
core::pack::task::PackerTaskOP  packer_task 
)
private
void protocols::ddg::ddGMover::setup_packertask ( core::pack::task::PackerTaskOP  pt,
core::pose::Pose p 
)
private
void protocols::ddg::ddGMover::setup_repack_constraints ( core::pose::Pose pose,
core::scoring::ScoreFunctionOP  sfxn,
bool  all_but_mut_site,
utility::vector1< char > &  constraints_at_pos 
)
private

sets up only rotamer constraints available during repacking

References core::chemical::aa_unk, core::scoring::atom_pair_constraint, core::pose::Pose::remove_constraints(), and residues_to_mutate_.

Referenced by relax_wildtype_structure().

void protocols::ddg::ddGMover::setup_rotamer_constraints ( core::pose::Pose p,
core::scoring::ScoreFunction s,
utility::vector1< int > &  mutation_position,
bool  all_but_mutation_site,
utility::vector1< char > &  constraints_at_pos 
)
private
int protocols::ddg::ddGMover::store_energies ( ObjexxFCL::FArray2D< double > &  two_d_e_arrays,
core::scoring::ScoreFunction s,
core::pose::Pose p,
int  next_index,
int  size_to_expect 
)
private
double protocols::ddg::ddGMover::sum ( ddGs scores_to_sum)
private
bool protocols::ddg::ddGMover::use_mean ( )

References mean_.

bool protocols::ddg::ddGMover::use_min ( )

References min_.

void protocols::ddg::ddGMover::wt_score_components ( ObjexxFCL::FArray2D< double >  wsc)

References wt_components_.

Referenced by protocols::ddG_main().

ObjexxFCL::FArray2D< double > protocols::ddg::ddGMover::wt_score_components ( )

References wt_components_.

void protocols::ddg::ddGMover::wt_unbound_score_components ( ObjexxFCL::FArray2D< double >  wusc)

References wt_unbound_components_.

Referenced by protocols::ddG_main().

ObjexxFCL::FArray2D< double > protocols::ddg::ddGMover::wt_unbound_score_components ( )

Member Data Documentation

core::scoring::constraints::ConstraintSetOP protocols::ddg::ddGMover::cst_set_
private

report the score with this score function

bool protocols::ddg::ddGMover::dbg_output_
private
bool protocols::ddg::ddGMover::dmp_pdb_
private
bool protocols::ddg::ddGMover::interface_ddg_
private
bool protocols::ddg::ddGMover::mean_
private
bool protocols::ddg::ddGMover::min_
private
bool protocols::ddg::ddGMover::min_cst_
private
utility::vector1<char> protocols::ddg::ddGMover::min_cst_mut_types_
private
core::scoring::constraints::ConstraintSetOP protocols::ddg::ddGMover::min_cst_set_mut_
private

Referenced by apply(), and relax_wildtype_structure().

core::scoring::constraints::ConstraintSetOP protocols::ddg::ddGMover::min_cst_set_wt_
private
core::scoring::ScoreFunctionOP protocols::ddg::ddGMover::min_cst_sfxn_
private
core::scoring::ScoreFunctionOP protocols::ddg::ddGMover::min_cst_sfxn_no_cst_weight_
private

minimize the score with this score function

Referenced by apply(), relax_wildtype_structure(), and set_minimization_score_function().

utility::vector1<char> protocols::ddg::ddGMover::min_cst_wt_types_
private
ObjexxFCL::FArray2D<double> protocols::ddg::ddGMover::mutant_components_
private
ObjexxFCL::FArray2D<double> protocols::ddg::ddGMover::mutant_unbound_components_
private
utility::vector1<pose::Pose> protocols::ddg::ddGMover::mutants_
private

Referenced by apply().

utility::vector1<pose::Pose> protocols::ddg::ddGMover::natives_
private
core::Real protocols::ddg::ddGMover::nbr_cutoff_
private
core::Real protocols::ddg::ddGMover::num_decoys_used_in_calculations_
private
int protocols::ddg::ddGMover::num_iterations_
private
core::scoring::constraints::ConstraintSetOP protocols::ddg::ddGMover::repack_cst_set_mut_
private

Referenced by apply(), and relax_wildtype_structure().

core::scoring::constraints::ConstraintSetOP protocols::ddg::ddGMover::repack_cst_set_wt_
private
utility::vector1<char> protocols::ddg::ddGMover::repack_mut_types_
private
utility::vector1<char> protocols::ddg::ddGMover::repack_wt_types_
private
utility::vector1<core::chemical::AA> protocols::ddg::ddGMover::residues_to_mutate_
private
bool protocols::ddg::ddGMover::restrict_to_nbrhood_
private
core::scoring::ScoreFunctionOP protocols::ddg::ddGMover::scorefxn_
private
ObjexxFCL::FArray2D<double> protocols::ddg::ddGMover::wt_components_
private
ObjexxFCL::FArray2D<double> protocols::ddg::ddGMover::wt_unbound_components_
private

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