Rosetta 3.4
Public Member Functions | Static Public Member Functions
protocols::noesy_assign::NoesyModule Class Reference

#include <NoesyModule.hh>

Inheritance diagram for protocols::noesy_assign::NoesyModule:
Inheritance graph
[legend]
Collaboration diagram for protocols::noesy_assign::NoesyModule:
Collaboration graph
[legend]

List of all members.

Public Member Functions

 NoesyModule (std::string const &fasta_sequence)
 Constructor - read input files / requires options to be initialized.
void assign (core::Size cycle)
 assign peaks ( no explicit decoys - wrapper )
void generate_constraint_files (core::pose::Pose const &pose, std::string const &cst_fa_file, std::string const &cst_centroid_file) const
 NoesyModule (std::string const &fasta_sequence)
 constructor -- initialize with fast-sequence
template<class DecoyIterator >
void assign (DecoyIterator const &begin, DecoyIterator const &end, core::Size cycle=0)
 assign NOE data, use models provided by DecoyIterator for scoring and restraint exclusion, if cycle=0 read cycle from cmd-line
void assign (core::Size cycle=0)
 same as above, but decoy file will be determined from commandline and read directly
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) const
 after assignment --> create appropriate constraints
void write_assignments (std::string file="use_cmd_line")
 write assignments into peak-file...
void reset ()
 reset assignments... -- call before re-assigning peaks
CrossPeakList const & crosspeaks () const
 return (cross)peak-list (peak-file)
ResonanceList const & resonances () const
 return resonance assignments (prot-file)

Static Public Member Functions

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

Constructor & Destructor Documentation

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

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

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

constructor -- initialize with fast-sequence


Member Function Documentation

void protocols::noesy_assign::NoesyModule::assign ( core::Size  cycle)

assign peaks ( no explicit decoys - wrapper )

References resonances(), protocols::noesy_assign::ResonanceList::sequence(), and protocols::kinmatch::str().

template<class DecoyIterator >
void protocols::noesy_assign::NoesyModule::assign ( DecoyIterator const &  begin,
DecoyIterator const &  end,
core::Size  cycle = 0 
)

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

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

void protocols::noesy_assign::NoesyModule::assign ( core::Size  cycle = 0)

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

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

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

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 
) const
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 
) const

after assignment --> create appropriate constraints

generate constraint files from assignments

References core::chemical::CENTROID, core::util::switch_to_residue_type_set(), tr(), and core::scoring::constraints::ConstraintIO::write_constraints().

void protocols::noesy_assign::NoesyModule::register_options ( ) [static]

register options

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()

ResonanceList const& protocols::noesy_assign::NoesyModule::resonances ( ) const [inline]

return resonance assignments (prot-file)

Referenced by assign().

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)


The documentation for this class was generated from the following files:
 All Classes Namespaces Files Functions Variables Typedefs Enumerations Enumerator Friends Defines