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protocols::stepwise::modeler::protein::StepWiseProteinBackboneSampler Class Reference

#include <StepWiseProteinBackboneSampler.hh>

Inheritance diagram for protocols::stepwise::modeler::protein::StepWiseProteinBackboneSampler:
Inheritance graph
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Public Member Functions

 StepWiseProteinBackboneSampler (protocols::stepwise::modeler::working_parameters::StepWiseWorkingParametersCOP working_parameters)
 
 ~StepWiseProteinBackboneSampler () override
 
void apply (core::pose::Pose &pose_to_visualize) override
 Apply the minimizer to one pose. More...
 
std::string get_name () const override
 Each derived class must specify its name. The class name. More...
 
void set_silent_file (std::string const &setting)
 
void set_rmsd_cutoff (core::Real const setting)
 
void set_n_sample (core::Size const setting)
 
void set_nstruct_centroid (core::Size const setting)
 
void set_filter_native_big_bins (bool const setting)
 
void set_centroid_screen (bool const setting)
 
void set_ghost_loops (bool const setting)
 
void set_apply_vdw_cut (bool const setting)
 
void set_centroid_scorefxn (core::scoring::ScoreFunctionOP const &scorefxn)
 
void set_centroid_score_diff_cut (core::Real const setting)
 
utility::vector1
< MainChainTorsionSetList >
const & 
main_chain_torsion_set_lists () const
 
utility::vector1
< utility::vector1< core::Real > > 
main_chain_torsion_set_lists_real (core::pose::Pose const &pose) const
 
utility::vector1
< core::id::TorsionID
which_torsions (core::pose::Pose const &pose)
 
void setup_centroid_screen (core::Real const centroid_score_diff_cut, std::string const &centroid_weights, core::Size const nstruct_centroid, bool const ghost_loops)
 
core::Size get_big_bin (core::Real const phi, core::Real const psi) const
 
void set_moving_residues (utility::vector1< core::Size > const &moving_res)
 
void set_fixed_residues (utility::vector1< core::Size > const &fixed_res)
 
void set_expand_loop_takeoff (bool const setting)
 
bool expand_loop_takeoff () const
 
- 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 Member Functions

void define_moving_res (core::pose::Pose const &pose)
 
void setup_torsion_sets (core::pose::Pose const &pose)
 
void filter_main_chain_torsion_sets ()
 
void prepare_ghost_pose (core::pose::Pose const &pose)
 
void initialize_ghost_pose (core::pose::PoseOP &ghost_pose, std::string const &desired_sequence, core::pose::Pose const &template_pose, ResMap const &ghost_map, core::kinematics::FoldTree f)
 
void copy_coords (core::pose::Pose &pose, core::pose::Pose const &template_pose, ResMap const &ghost_map) const
 
core::kinematics::FoldTree figure_out_fold_tree (ResMap const &ghost_map) const
 
void sample_residues_recursively (core::Size const which_res, core::Size &count, core::pose::Pose &pose)
 
void filter_and_save (core::pose::Pose &pose, std::string const &tag)
 
void get_main_chain_torsion_set_list (core::Size const n, core::pose::Pose const &pose, MainChainTorsionSetList &main_chain_torsion_set_list)
 
void get_main_chain_torsion_set_list_coarse (core::Size const n, core::pose::Pose const &pose, MainChainTorsionSetList &main_chain_torsion_set_list)
 
void get_main_chain_torsion_set_list_full (core::Size const n, core::pose::Pose const &pose, core::Real const best_energy_cutoff, MainChainTorsionSetList &main_chain_torsion_set_list)
 
void get_main_chain_torsion_set_list_n_terminus (core::Size const n, core::pose::Pose const &pose, core::Real const best_energy_cutoff, MainChainTorsionSetList &main_chain_torsion_set_list)
 
void get_main_chain_torsion_set_list_c_terminus (core::Size const n, core::pose::Pose const &pose, core::Real const best_energy_cutoff, MainChainTorsionSetList &main_chain_torsion_set_list)
 
void get_main_chain_torsion_set_list_sample_phi_only (core::Size const n, core::pose::Pose const &pose, core::Real const best_energy_cutoff, MainChainTorsionSetList &main_chain_torsion_set_list)
 
void get_main_chain_torsion_set_list_sample_psi_only (core::Size const n, core::pose::Pose const &pose, core::Real const best_energy_cutoff, MainChainTorsionSetList &main_chain_torsion_set_list)
 
void filter_native_BIG_BINS (core::Size const n, MainChainTorsionSetList &main_chain_torsion_set_list)
 
void filter_based_on_desired_secstruct (char const secstruct, MainChainTorsionSetList &main_chain_torsion_set_list)
 
void filter_big_bin (core::Size const big_bin, MainChainTorsionSetList &main_chain_torsion_set_list)
 
void output_centroid_silent_struct (core::pose::Pose const &pose, core::pose::PoseCOP const &native_pose_op, std::string const &silent_file, std::string const &tag)
 
void convert_to_centroid (core::pose::Pose &pose)
 
void sample_cis_omega (MainChainTorsionSetList &main_chain_torsion_set_list)
 
void initialize_is_fixed_res ()
 
core::Real get_rotamer_angle (core::Size const i, core::Size const N_SAMPLE)
 
core::Real rama_energy (core::Size const n, core::pose::Pose const &pose, utility::vector1< core::Real > const &mainchain_torsions)
 

Private Attributes

protocols::stepwise::modeler::working_parameters::StepWiseWorkingParametersCOP working_parameters_
 
utility::vector1< core::Size >
const 
moving_residues_input_
 
utility::vector1< core::Sizemoving_residues_
 
core::Size n_sample_
 
core::Size n_sample_beta_
 
core::Real rmsd_cutoff_
 
core::scoring::ScoreFunctionOP centroid_scorefxn_
 
std::string silent_file_
 
bool filter_native_big_bins_
 
bool centroid_screen_
 
core::Real centroid_score_ref_
 
core::Real centroid_score_diff_cut_
 
bool apply_vdw_cut_
 
core::Real centroid_vdw_ref_
 
core::Size nstruct_centroid_
 
core::scoring::Ramachandran const & ramachandran_
 
core::scoring::RamaPrePro const & rama_pre_pro_
 
MainChainTorsionSetList main_chain_torsion_set_for_moving_residues_
 
utility::vector1
< MainChainTorsionSetList
main_chain_torsion_sets_for_moving_residues_
 
utility::vector1< core::Realcentroid_scores_
 
bool ghost_loops_
 
ResMap ghost_map_
 
core::pose::PoseOP ghost_pose_
 
core::pose::PoseOP ghost_native_pose_
 
utility::vector1< boolis_pre_proline_
 
utility::vector1< boolis_fixed_res_
 
utility::vector1< boolis_fixed_res_input_
 
bool expand_loop_takeoff_
 
bool use_rama_pre_pro_
 

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::stepwise::modeler::protein::StepWiseProteinBackboneSampler::StepWiseProteinBackboneSampler ( protocols::stepwise::modeler::working_parameters::StepWiseWorkingParametersCOP  working_parameters)
protocols::stepwise::modeler::protein::StepWiseProteinBackboneSampler::~StepWiseProteinBackboneSampler ( )
overridedefault

Member Function Documentation

void protocols::stepwise::modeler::protein::StepWiseProteinBackboneSampler::apply ( core::pose::Pose pose_to_visualize)
overridevirtual
void protocols::stepwise::modeler::protein::StepWiseProteinBackboneSampler::convert_to_centroid ( core::pose::Pose pose)
private
void protocols::stepwise::modeler::protein::StepWiseProteinBackboneSampler::copy_coords ( core::pose::Pose pose,
core::pose::Pose const &  template_pose,
ResMap const &  ghost_map 
) const
private
void protocols::stepwise::modeler::protein::StepWiseProteinBackboneSampler::define_moving_res ( core::pose::Pose const &  pose)
private
bool protocols::stepwise::modeler::protein::StepWiseProteinBackboneSampler::expand_loop_takeoff ( ) const
inline

References expand_loop_takeoff_.

core::kinematics::FoldTree protocols::stepwise::modeler::protein::StepWiseProteinBackboneSampler::figure_out_fold_tree ( ResMap const &  ghost_map) const
private
void protocols::stepwise::modeler::protein::StepWiseProteinBackboneSampler::filter_and_save ( core::pose::Pose pose,
std::string const &  tag 
)
private
void protocols::stepwise::modeler::protein::StepWiseProteinBackboneSampler::filter_based_on_desired_secstruct ( char const  secstruct,
MainChainTorsionSetList main_chain_torsion_set_list 
)
private
void protocols::stepwise::modeler::protein::StepWiseProteinBackboneSampler::filter_big_bin ( core::Size const  big_bin,
MainChainTorsionSetList main_chain_torsion_set_list 
)
private
void protocols::stepwise::modeler::protein::StepWiseProteinBackboneSampler::filter_main_chain_torsion_sets ( )
private
void protocols::stepwise::modeler::protein::StepWiseProteinBackboneSampler::filter_native_BIG_BINS ( core::Size const  n,
MainChainTorsionSetList main_chain_torsion_set_list 
)
private
Size protocols::stepwise::modeler::protein::StepWiseProteinBackboneSampler::get_big_bin ( core::Real const  phi,
core::Real const  psi 
) const
void protocols::stepwise::modeler::protein::StepWiseProteinBackboneSampler::get_main_chain_torsion_set_list ( core::Size const  n,
core::pose::Pose const &  pose,
MainChainTorsionSetList main_chain_torsion_set_list 
)
private
void protocols::stepwise::modeler::protein::StepWiseProteinBackboneSampler::get_main_chain_torsion_set_list_c_terminus ( core::Size const  n,
core::pose::Pose const &  pose,
core::Real const  best_energy_cutoff,
MainChainTorsionSetList main_chain_torsion_set_list 
)
private
void protocols::stepwise::modeler::protein::StepWiseProteinBackboneSampler::get_main_chain_torsion_set_list_coarse ( core::Size const  n,
core::pose::Pose const &  pose,
MainChainTorsionSetList main_chain_torsion_set_list 
)
private
void protocols::stepwise::modeler::protein::StepWiseProteinBackboneSampler::get_main_chain_torsion_set_list_full ( core::Size const  n,
core::pose::Pose const &  pose,
core::Real const  best_energy_cutoff,
MainChainTorsionSetList main_chain_torsion_set_list 
)
private
void protocols::stepwise::modeler::protein::StepWiseProteinBackboneSampler::get_main_chain_torsion_set_list_n_terminus ( core::Size const  n,
core::pose::Pose const &  pose,
core::Real const  best_energy_cutoff,
MainChainTorsionSetList main_chain_torsion_set_list 
)
private
void protocols::stepwise::modeler::protein::StepWiseProteinBackboneSampler::get_main_chain_torsion_set_list_sample_phi_only ( core::Size const  n,
core::pose::Pose const &  pose,
core::Real const  best_energy_cutoff,
MainChainTorsionSetList main_chain_torsion_set_list 
)
private
void protocols::stepwise::modeler::protein::StepWiseProteinBackboneSampler::get_main_chain_torsion_set_list_sample_psi_only ( core::Size const  n,
core::pose::Pose const &  pose,
core::Real const  best_energy_cutoff,
MainChainTorsionSetList main_chain_torsion_set_list 
)
private
std::string protocols::stepwise::modeler::protein::StepWiseProteinBackboneSampler::get_name ( ) const
overridevirtual

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

Implements protocols::moves::Mover.

Real protocols::stepwise::modeler::protein::StepWiseProteinBackboneSampler::get_rotamer_angle ( core::Size const  i,
core::Size const  N_SAMPLE 
)
private
void protocols::stepwise::modeler::protein::StepWiseProteinBackboneSampler::initialize_ghost_pose ( core::pose::PoseOP ghost_pose,
std::string const &  desired_sequence,
core::pose::Pose const &  template_pose,
ResMap const &  ghost_map,
core::kinematics::FoldTree  f 
)
private
void protocols::stepwise::modeler::protein::StepWiseProteinBackboneSampler::initialize_is_fixed_res ( )
private
utility::vector1< MainChainTorsionSetList > const & protocols::stepwise::modeler::protein::StepWiseProteinBackboneSampler::main_chain_torsion_set_lists ( ) const
utility::vector1< utility::vector1< core::Real > > protocols::stepwise::modeler::protein::StepWiseProteinBackboneSampler::main_chain_torsion_set_lists_real ( core::pose::Pose const &  pose) const
void protocols::stepwise::modeler::protein::StepWiseProteinBackboneSampler::output_centroid_silent_struct ( core::pose::Pose const &  pose,
core::pose::PoseCOP const &  native_pose_op,
std::string const &  silent_file,
std::string const &  tag 
)
private
void protocols::stepwise::modeler::protein::StepWiseProteinBackboneSampler::prepare_ghost_pose ( core::pose::Pose const &  pose)
private
Real protocols::stepwise::modeler::protein::StepWiseProteinBackboneSampler::rama_energy ( core::Size const  n,
core::pose::Pose const &  pose,
utility::vector1< core::Real > const &  mainchain_torsions 
)
private
void protocols::stepwise::modeler::protein::StepWiseProteinBackboneSampler::sample_cis_omega ( MainChainTorsionSetList main_chain_torsion_set_list)
private
void protocols::stepwise::modeler::protein::StepWiseProteinBackboneSampler::sample_residues_recursively ( core::Size const  which_res,
core::Size count,
core::pose::Pose pose 
)
private
void protocols::stepwise::modeler::protein::StepWiseProteinBackboneSampler::set_apply_vdw_cut ( bool const  setting)

References apply_vdw_cut_.

Referenced by setup_centroid_screen().

void protocols::stepwise::modeler::protein::StepWiseProteinBackboneSampler::set_centroid_score_diff_cut ( core::Real const  setting)
void protocols::stepwise::modeler::protein::StepWiseProteinBackboneSampler::set_centroid_scorefxn ( core::scoring::ScoreFunctionOP const &  scorefxn)

References centroid_scorefxn_.

Referenced by setup_centroid_screen().

void protocols::stepwise::modeler::protein::StepWiseProteinBackboneSampler::set_centroid_screen ( bool const  setting)

References centroid_screen_.

Referenced by setup_centroid_screen().

void protocols::stepwise::modeler::protein::StepWiseProteinBackboneSampler::set_expand_loop_takeoff ( bool const  setting)
inline
void protocols::stepwise::modeler::protein::StepWiseProteinBackboneSampler::set_filter_native_big_bins ( bool const  setting)
void protocols::stepwise::modeler::protein::StepWiseProteinBackboneSampler::set_fixed_residues ( utility::vector1< core::Size > const &  fixed_res)
void protocols::stepwise::modeler::protein::StepWiseProteinBackboneSampler::set_ghost_loops ( bool const  setting)

References ghost_loops_.

Referenced by setup_centroid_screen().

void protocols::stepwise::modeler::protein::StepWiseProteinBackboneSampler::set_moving_residues ( utility::vector1< core::Size > const &  moving_res)

References moving_residues_.

void protocols::stepwise::modeler::protein::StepWiseProteinBackboneSampler::set_n_sample ( core::Size const  setting)
void protocols::stepwise::modeler::protein::StepWiseProteinBackboneSampler::set_nstruct_centroid ( core::Size const  setting)

References nstruct_centroid_.

Referenced by setup_centroid_screen().

void protocols::stepwise::modeler::protein::StepWiseProteinBackboneSampler::set_rmsd_cutoff ( core::Real const  setting)

References rmsd_cutoff_.

void protocols::stepwise::modeler::protein::StepWiseProteinBackboneSampler::set_silent_file ( std::string const &  setting)
void protocols::stepwise::modeler::protein::StepWiseProteinBackboneSampler::setup_centroid_screen ( core::Real const  centroid_score_diff_cut,
std::string const &  centroid_weights,
core::Size const  nstruct_centroid,
bool const  ghost_loops 
)
void protocols::stepwise::modeler::protein::StepWiseProteinBackboneSampler::setup_torsion_sets ( core::pose::Pose const &  pose)
private
utility::vector1< id::TorsionID > protocols::stepwise::modeler::protein::StepWiseProteinBackboneSampler::which_torsions ( core::pose::Pose const &  pose)

Member Data Documentation

bool protocols::stepwise::modeler::protein::StepWiseProteinBackboneSampler::apply_vdw_cut_
private
core::Real protocols::stepwise::modeler::protein::StepWiseProteinBackboneSampler::centroid_score_diff_cut_
private
core::Real protocols::stepwise::modeler::protein::StepWiseProteinBackboneSampler::centroid_score_ref_
private
core::scoring::ScoreFunctionOP protocols::stepwise::modeler::protein::StepWiseProteinBackboneSampler::centroid_scorefxn_
private
utility::vector1< core::Real > protocols::stepwise::modeler::protein::StepWiseProteinBackboneSampler::centroid_scores_
private
bool protocols::stepwise::modeler::protein::StepWiseProteinBackboneSampler::centroid_screen_
private
core::Real protocols::stepwise::modeler::protein::StepWiseProteinBackboneSampler::centroid_vdw_ref_
private
bool protocols::stepwise::modeler::protein::StepWiseProteinBackboneSampler::expand_loop_takeoff_
private
bool protocols::stepwise::modeler::protein::StepWiseProteinBackboneSampler::filter_native_big_bins_
private
bool protocols::stepwise::modeler::protein::StepWiseProteinBackboneSampler::ghost_loops_
private
ResMap protocols::stepwise::modeler::protein::StepWiseProteinBackboneSampler::ghost_map_
private
core::pose::PoseOP protocols::stepwise::modeler::protein::StepWiseProteinBackboneSampler::ghost_native_pose_
private

Referenced by prepare_ghost_pose().

core::pose::PoseOP protocols::stepwise::modeler::protein::StepWiseProteinBackboneSampler::ghost_pose_
private
utility::vector1< bool > protocols::stepwise::modeler::protein::StepWiseProteinBackboneSampler::is_fixed_res_
private
utility::vector1< bool > protocols::stepwise::modeler::protein::StepWiseProteinBackboneSampler::is_fixed_res_input_
private
utility::vector1< bool > protocols::stepwise::modeler::protein::StepWiseProteinBackboneSampler::is_pre_proline_
private
MainChainTorsionSetList protocols::stepwise::modeler::protein::StepWiseProteinBackboneSampler::main_chain_torsion_set_for_moving_residues_
private
utility::vector1< MainChainTorsionSetList > protocols::stepwise::modeler::protein::StepWiseProteinBackboneSampler::main_chain_torsion_sets_for_moving_residues_
private
utility::vector1< core::Size > protocols::stepwise::modeler::protein::StepWiseProteinBackboneSampler::moving_residues_
private
utility::vector1< core::Size > const protocols::stepwise::modeler::protein::StepWiseProteinBackboneSampler::moving_residues_input_
private

Referenced by define_moving_res().

core::Size protocols::stepwise::modeler::protein::StepWiseProteinBackboneSampler::n_sample_
private
core::Size protocols::stepwise::modeler::protein::StepWiseProteinBackboneSampler::n_sample_beta_
private
core::Size protocols::stepwise::modeler::protein::StepWiseProteinBackboneSampler::nstruct_centroid_
private
core::scoring::RamaPrePro const& protocols::stepwise::modeler::protein::StepWiseProteinBackboneSampler::rama_pre_pro_
private

Referenced by rama_energy().

core::scoring::Ramachandran const& protocols::stepwise::modeler::protein::StepWiseProteinBackboneSampler::ramachandran_
private

Referenced by rama_energy().

core::Real protocols::stepwise::modeler::protein::StepWiseProteinBackboneSampler::rmsd_cutoff_
private

Referenced by filter_and_save(), and set_rmsd_cutoff().

std::string protocols::stepwise::modeler::protein::StepWiseProteinBackboneSampler::silent_file_
private

Referenced by set_silent_file().

bool protocols::stepwise::modeler::protein::StepWiseProteinBackboneSampler::use_rama_pre_pro_
private

Referenced by rama_energy().

protocols::stepwise::modeler::working_parameters::StepWiseWorkingParametersCOP protocols::stepwise::modeler::protein::StepWiseProteinBackboneSampler::working_parameters_
private

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