#include <NoesyModule.hh>

Public Member Functions
	NoesyModule (std::string const &fasta_sequence)
	Constructor - read input files / requires options to be initialized. More...

void	assign (core::Size cycle)

void	generate_constraint_files (core::pose::Pose const &pose, std::string const &cst_fa_file, std::string const &cst_centroid_file) const

virtual	~NoesyModule ()
	Automatically generated virtual destructor for class deriving directly from ReferenceCount. 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...

ResonanceListOP	resonances_

std::string	sequence_

Static Private Attributes
static bool	options_registered_

Constructor & Destructor Documentation

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

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

References utility::io::izstream::good(), basic::options::option, output_file, and protocols::noesy_assign::tr.

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

virtual

Automatically generated virtual destructor for class deriving directly from ReferenceCount.

Auto-generated virtual destructor

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

constructor – initialize with fast-sequence

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_.

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

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_, protocols::noesy_assign::PeakAssignmentParameters::no_network_, and params.

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 option, sequence(), protocols::kinmatch::str(), user, and utility_exit_with_message.

bool protocols::noesy_assign::NoesyModule::cmdline_options_activated ( )

static

returns true if -noesy::in::resonances and -noesy::in::peaks are in cmd-line

References basic::options::option, and user.

Referenced by protocols::simple_filters::RPF_ScoreEvaluator::apply(), protocols::abinitio::IterativeBase::gen_evaluation_output(), protocols::abinitio::IterativeBase::gen_noe_assignments(), protocols::abinitio::IterativeBase::idle(), protocols::abinitio::IterativeFullatom::initialize(), protocols::abinitio::IterativeBase::reassign_noesy_data(), protocols::abinitio::IterativeBase::replace_noesy_filter_constraints(), and protocols::abinitio::IterativeBase::setup_autoNOE().

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
	)		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,
		core::Size	min_quali = `0`,
		core::Size	max_quali = `4`,
		bool	ignore_elimination_candidates = `true`,
		bool	elimination_candidates = `false`
	)		const