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Public Member Functions | Private Member Functions | Private Attributes | List of all members
RNA_DeNovoJobQueen Class Reference
Inheritance diagram for RNA_DeNovoJobQueen:
Inheritance graph
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Public Member Functions

 RNA_DeNovoJobQueen ()
 
virtual JobOP complete_larval_job_maturation (protocols::jd3::LarvalJobCOP larval_job, utility::options::OptionCollectionCOP job_options, utility::vector1< JobResultCOP > const &)
 
void initialize_scorefxn (core::pose::Pose &pose)
 
void initialize_constraints (core::pose::Pose &pose)
 
void calc_rmsds (core::io::silent::SilentStruct &s, core::pose::Pose &pose, std::string const &out_file_tag) const
 
void output_silent_struct (core::io::silent::SilentStruct &s, core::io::silent::SilentFileData &silent_file_data, std::string const &silent_file, pose::Pose &pose, std::string const &out_file_tag, bool const score_only) const
 
void output_to_silent_file (core::pose::Pose &pose, std::string const &silent_file, std::string const &out_file_tag, bool const score_only) const
 
void align_and_output_to_silent_file (core::pose::Pose &pose, std::string const &silent_file, std::string const &out_file_tag) const
 
void add_chem_shift_info (core::io::silent::SilentStruct &silent_struct, core::pose::Pose const &const_pose) const
 

Private Member Functions

pose::PoseCOP get_native_pose () const
 

Private Attributes

core::import_pose::options::RNA_DeNovoProtocolOptionsCOP options_
 
core::import_pose::RNA_DeNovoParametersCOP rna_params_
 
protocols::stepwise::modeler::rna::checker::RNA_VDW_BinCheckerOP vdw_grid_
 
std::string lores_silent_file_
 
RNA_FragmentMonteCarloOP rna_fragment_monte_carlo_
 
std::map< std::string, booltag_is_done_
 
core::scoring::ScoreFunctionOP denovo_scorefxn_
 
core::scoring::ScoreFunctionOP hires_scorefxn_
 
utility::vector1
< core::pose::PoseOP > 
refine_pose_list_
 
pose::PoseCOP native_pose_
 

Constructor & Destructor Documentation

RNA_DeNovoJobQueen::RNA_DeNovoJobQueen ( )
inline

Member Function Documentation

void RNA_DeNovoJobQueen::add_chem_shift_info ( core::io::silent::SilentStruct &  silent_struct,
core::pose::Pose const &  const_pose 
) const
inline
void RNA_DeNovoJobQueen::align_and_output_to_silent_file ( core::pose::Pose pose,
std::string const &  silent_file,
std::string const &  out_file_tag 
) const
inline
void RNA_DeNovoJobQueen::calc_rmsds ( core::io::silent::SilentStruct &  s,
core::pose::Pose pose,
std::string const &  out_file_tag 
) const
inline
virtual JobOP RNA_DeNovoJobQueen::complete_larval_job_maturation ( protocols::jd3::LarvalJobCOP  larval_job,
utility::options::OptionCollectionCOP  job_options,
utility::vector1< JobResultCOP > const &   
)
inlinevirtual
pose::PoseCOP RNA_DeNovoJobQueen::get_native_pose ( ) const
inlineprivate
void RNA_DeNovoJobQueen::initialize_constraints ( core::pose::Pose pose)
inline
void RNA_DeNovoJobQueen::initialize_scorefxn ( core::pose::Pose pose)
inline
void RNA_DeNovoJobQueen::output_silent_struct ( core::io::silent::SilentStruct &  s,
core::io::silent::SilentFileData &  silent_file_data,
std::string const &  silent_file,
pose::Pose pose,
std::string const &  out_file_tag,
bool const  score_only 
) const
inline
void RNA_DeNovoJobQueen::output_to_silent_file ( core::pose::Pose pose,
std::string const &  silent_file,
std::string const &  out_file_tag,
bool const  score_only 
) const
inline

Member Data Documentation

core::scoring::ScoreFunctionOP RNA_DeNovoJobQueen::denovo_scorefxn_
private
core::scoring::ScoreFunctionOP RNA_DeNovoJobQueen::hires_scorefxn_
private
std::string RNA_DeNovoJobQueen::lores_silent_file_
private
pose::PoseCOP RNA_DeNovoJobQueen::native_pose_
private
core::import_pose::options::RNA_DeNovoProtocolOptionsCOP RNA_DeNovoJobQueen::options_
private
utility::vector1<core::pose::PoseOP> RNA_DeNovoJobQueen::refine_pose_list_
private
RNA_FragmentMonteCarloOP RNA_DeNovoJobQueen::rna_fragment_monte_carlo_
private
core::import_pose::RNA_DeNovoParametersCOP RNA_DeNovoJobQueen::rna_params_
private
std::map< std::string, bool > RNA_DeNovoJobQueen::tag_is_done_
private
protocols::stepwise::modeler::rna::checker::RNA_VDW_BinCheckerOP RNA_DeNovoJobQueen::vdw_grid_
private

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