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:

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

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

Referenced by 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,
		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

return all input files

read peak- and resonance files

References crosspeaks_, sequence(), protocols::noesy_assign::PeakFileFormat_Base::set_filename(), protocols::noesy_assign::PeakFileFormat_Base::set_ignore_assignments(), and protocols::noesy_assign::tr().

Referenced by NoesyModule(), and reset().

void protocols::noesy_assign::NoesyModule::register_options ( )

static

register options

References protocols::evaluation::options_registered_, and protocols::evaluation::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()

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().

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

• src/protocols/noesy_assign/NoesyModule.hh
• src/protocols/noesy_assign/NoesyModule.cc
• src/protocols/noesy_assign/NoesyModule.impl.hh