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protocols::noesy_assign::NoesyModule Class Reference

WARNING WARNING WARNING THREAD UNSAFE FOR USING THE COVALENTCOMPLIANCE CLASS IN A NON-CONST WAY. More...

#include <NoesyModule.hh>

Inheritance diagram for protocols::noesy_assign::NoesyModule:
Inheritance graph
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Public Member Functions

 ~NoesyModule () override
 Automatically generated virtual destructor for class deriving directly from VirtualBase. More...
 
 NoesyModule (std::string const &fasta_sequence)
 constructor – initialize with fast-sequence More...
 
template<class DecoyIterator >
void assign (DecoyIterator const &begin, DecoyIterator const &end)
 assign NOE data, use models provided by DecoyIterator for scoring and restraint exclusion, if cycle=0 read cycle from cmd-line More...
 
void assign ()
 same as above, but decoy file will be determined from commandline and read directly More...
 
void generate_constraint_files (core::pose::Pose const &pose, std::string const &cst_fa_file, std::string const &cst_centroid_file, core::Size min_seq_separation, core::Size min_quali=0, core::Size max_quali=4, bool ignore_elimination_candidates=true, bool elimination_candidates=false) const
 after assignment –> create appropriate constraints More...
 
void write_assignments (std::string file="use_cmd_line")
 write assignments into peak-file... More...
 
void reset ()
 reset assignments... – call before re-assigning peaks More...
 
CrossPeakList const & crosspeaks () const
 return (cross)peak-list (peak-file) More...
 
void add_dist_viol_to_assignments (core::pose::Pose native_pose)
 return resonance assignments (prot-file) More...
 
std::string const & sequence ()
 

Static Public Member Functions

static void register_options ()
 register options More...
 
static bool cmdline_options_activated ()
 returns true if -noesy::in::resonances and -noesy::in::peaks are in cmd-line More...
 

Private Member Functions

void read_input_files ()
 return all input files More...
 

Private Attributes

CrossPeakListOP crosspeaks_
 private data, peak-list and master-resonances (sometimes different resonances for different peak-lists, thus the name) More...
 
std::string sequence_
 

Static Private Attributes

static bool options_registered_
 

Detailed Description

WARNING WARNING WARNING THREAD UNSAFE FOR USING THE COVALENTCOMPLIANCE CLASS IN A NON-CONST WAY.

Constructor & Destructor Documentation

protocols::noesy_assign::NoesyModule::~NoesyModule ( )
overridedefault

Automatically generated virtual destructor for class deriving directly from VirtualBase.

Auto-generated virtual destructor

protocols::noesy_assign::NoesyModule::NoesyModule ( std::string const &  fasta_sequence)

constructor – initialize with fast-sequence

Constructor - read input files / requires options to be initialized.

References options_registered_, and read_input_files().

Member Function Documentation

void protocols::noesy_assign::NoesyModule::add_dist_viol_to_assignments ( core::pose::Pose  native_pose)

return resonance assignments (prot-file)

References crosspeaks_.

template<class DecoyIterator >
void protocols::noesy_assign::NoesyModule::assign ( DecoyIterator const &  begin,
DecoyIterator const &  end 
)

assign NOE data, use models provided by DecoyIterator for scoring and restraint exclusion, if cycle=0 read cycle from cmd-line

References crosspeaks_, protocols::noesy_assign::PeakAssignmentParameters::get_instance(), protocols::noesy_assign::PeakAssignmentParameters::min_contribution_symmetric_peaks_, and protocols::noesy_assign::PeakAssignmentParameters::no_network_.

void protocols::noesy_assign::NoesyModule::assign ( )

same as above, but decoy file will be determined from commandline and read directly

assign peaks ( no explicit decoys - wrapper )

References core::io::silent::SilentFileData::begin(), core::io::silent::SilentFileData::end(), core::io::silent::SilentFileData::read_file(), sequence(), core::io::silent::SilentFileData::size(), and protocols::kinmatch::str().

static bool protocols::noesy_assign::NoesyModule::cmdline_options_activated ( )
static
CrossPeakList const& protocols::noesy_assign::NoesyModule::crosspeaks ( ) const
inline

return (cross)peak-list (peak-file)

References crosspeaks_.

void protocols::noesy_assign::NoesyModule::generate_constraint_files ( core::pose::Pose const &  pose,
std::string const &  cst_fa_file,
std::string const &  cst_centroid_file,
core::Size  min_seq_separation,
core::Size  min_quali = 0,
core::Size  max_quali = 4,
bool  ignore_elimination_candidates = true,
bool  elimination_candidates = false 
) const

after assignment –> create appropriate constraints

generate constraint files from assignments

References core::chemical::CENTROID_t, crosspeaks_, core::util::switch_to_residue_type_set(), and protocols::noesy_assign::tr().

void protocols::noesy_assign::NoesyModule::read_input_files ( )
private
void protocols::noesy_assign::NoesyModule::register_options ( )
static
void protocols::noesy_assign::NoesyModule::reset ( void  )

reset assignments... – call before re-assigning peaks

delete all data and read input files again... aka fresh_instance()

References crosspeaks_, and read_input_files().

std::string const& protocols::noesy_assign::NoesyModule::sequence ( )
inline

References sequence_.

Referenced by assign(), and read_input_files().

void protocols::noesy_assign::NoesyModule::write_assignments ( std::string  file = "use_cmd_line")

write assignments into peak-file...

write peak assignments into peak-file (sparky, cyana)

References crosspeaks_.

Member Data Documentation

CrossPeakListOP protocols::noesy_assign::NoesyModule::crosspeaks_
private

private data, peak-list and master-resonances (sometimes different resonances for different peak-lists, thus the name)

Referenced by add_dist_viol_to_assignments(), assign(), crosspeaks(), generate_constraint_files(), read_input_files(), reset(), and write_assignments().

bool protocols::noesy_assign::NoesyModule::options_registered_
staticprivate

Referenced by NoesyModule().

std::string protocols::noesy_assign::NoesyModule::sequence_
private

Referenced by sequence().


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