protocols::analysis Namespace Reference

Classes
class	InterfaceAnalyzerMover
	Class for analyzing interfaces of a pose. Many metrics are calculated and accessible after the apply method. More...
class	InterfaceAnalyzerMoverCreator
struct	InterfaceData
	All interface data. Unless otherwise specified, they refer specifically to the interface. More...
class	LoopAnalyzerMover
class	PackStatMover
class	PeptideDeriverBasicStreamOutputter
	outputs a Peptiderive report to a stream in a basic, easily parsable format More...
class	PeptideDeriverFilter
	implementation of the Peptiderive protocol - given a pose, it evaluates the binding energy of linear stretches, of given lengths, and indicates which of these contributes more than others to the interaction energy. It also reports on and optionally models cyclizable peptides. More...
class	PeptideDeriverFilterCreator
class	PeptideDeriverMarkdownStreamOutputter
	outputs a Markdown formatted Peptiderive report to a stream More...
class	PeptideDeriverOutputter
	an abstract base class for handling calculation outputs from PeptideDeriverFilter Since PeptideDeriverFilter might have a set of outputs for each residue, for each chain in each chain-pair, outputting is quite elaborate. This is an attempt to decouple the calculation from the representation of results. Representation of results is delegated to implementors of this class. More...
class	PeptideDeriverOutputterContainer
	a container class which holds a list of PeptideDeriverOutputter instances and delegates calls to those. More...
class	PeptideDeriverPoseOutputter
	outputs poses at different points of the Peptiderive protocol, according to the given set of options More...
struct	PerResidueInterfaceData
	All per residue interface data and residue averages. Interface Residues only. More...

Typedefs
typedef utility::pointer::shared_ptr < InterfaceAnalyzerMover >	InterfaceAnalyzerMoverOP
typedef utility::pointer::shared_ptr < InterfaceAnalyzerMover const >	InterfaceAnalyzerMoverCOP
typedef utility::pointer::shared_ptr < LoopAnalyzerMover >	LoopAnalyzerMoverOP
typedef utility::pointer::shared_ptr < PackStatMover >	PackStatMoverOP
typedef utility::pointer::shared_ptr < PeptideDeriverFilter >	PeptideDeriverFilterOP
typedef utility::pointer::shared_ptr < PeptideDeriverFilter const >	PeptideDeriverFilterCOP
typedef utility::pointer::shared_ptr < PeptideDeriverOutputter >	PeptideDeriverOutputterOP
typedef utility::pointer::shared_ptr < PeptideDeriverOutputter const >	PeptideDeriverOutputterCOP
typedef utility::pointer::owning_ptr < PeptideDeriverFilterCreator >	PeptideDeriverFilterCreatorOP
typedef utility::pointer::owning_ptr < PeptideDeriverFilterCreator const >	PeptideDeriverFilterCreatorCOP

Enumerations
enum	InterfaceRegion { total = 1, side1, side2 }
enum	PeptideDeriverEntryType { ET_GENERAL, ET_BEST_LINEAR, ET_BEST_CYCLIC }
	an enum specifying whether the peptide entry encountered during the sliding window run in known to be the "best" peptide, when calling PeptideDeriverOuputter::peptide_entry() More...
enum	PeptideDeriverReportFormat { PRF_MARKDOWN, PRF_BASIC }
	the output format that PeptideDeriverFilter reports in More...

Functions
std::ostream &	which_ostream (std::ostream &ost, std::ostream &oss, bool const tracer)
	stupid helper function needed because ternary operator does not allow variable return types More...
static THREAD_LOCAL basic::Tracer	tracer ("protocols.analysis.PeptideDeriverFilter")
core::Real	avoid_negative_zero (core::Real const value, core::Real const threshold)

Typedef Documentation

typedef utility::pointer::shared_ptr< InterfaceAnalyzerMover const > protocols::analysis::InterfaceAnalyzerMoverCOP

typedef utility::pointer::shared_ptr< InterfaceAnalyzerMover > protocols::analysis::InterfaceAnalyzerMoverOP

typedef utility::pointer::shared_ptr< LoopAnalyzerMover > protocols::analysis::LoopAnalyzerMoverOP

typedef utility::pointer::shared_ptr< PackStatMover > protocols::analysis::PackStatMoverOP

typedef utility::pointer::shared_ptr<PeptideDeriverFilter const> protocols::analysis::PeptideDeriverFilterCOP

typedef utility::pointer::owning_ptr< PeptideDeriverFilterCreator const > protocols::analysis::PeptideDeriverFilterCreatorCOP

typedef utility::pointer::owning_ptr< PeptideDeriverFilterCreator > protocols::analysis::PeptideDeriverFilterCreatorOP

typedef utility::pointer::shared_ptr<PeptideDeriverFilter> protocols::analysis::PeptideDeriverFilterOP

typedef utility::pointer::shared_ptr<PeptideDeriverOutputter const> protocols::analysis::PeptideDeriverOutputterCOP

typedef utility::pointer::shared_ptr<PeptideDeriverOutputter> protocols::analysis::PeptideDeriverOutputterOP

Enumeration Type Documentation

enum protocols::analysis::InterfaceRegion

Enumerator
total
side1
side2

enum protocols::analysis::PeptideDeriverEntryType

an enum specifying whether the peptide entry encountered during the sliding window run in known to be the "best" peptide, when calling PeptideDeriverOuputter::peptide_entry()

Enumerator
ET_GENERAL	a peptide from the sliding window run
ET_BEST_LINEAR	the peptide whose linear model had the best interface score
ET_BEST_CYCLIC	the cyclizable peptide whose cyclic model had the best interface score, or, if no cyclic models were produced, the cyclizable peptide whose linear model had the best interface score.

enum protocols::analysis::PeptideDeriverReportFormat

the output format that PeptideDeriverFilter reports in

Enumerator
PRF_MARKDOWN	a pretty, readable but verbose format (Markdown)
PRF_BASIC	a stripped-down, easily parsable format

Function Documentation

core::Real protocols::analysis::avoid_negative_zero	(	core::Real const	value,
		core::Real const	threshold
	)

Referenced by protocols::analysis::PeptideDeriverBasicStreamOutputter::begin_receptor_partner_pair(), protocols::analysis::PeptideDeriverBasicStreamOutputter::peptide_entry(), protocols::analysis::PeptideDeriverMarkdownStreamOutputter::peptide_entry(), and protocols::analysis::PeptideDeriverMarkdownStreamOutputter::peptide_length().

static THREAD_LOCAL basic::Tracer protocols::analysis::tracer ( "protocols.analysis.PeptideDeriverFilter"  )

static

Referenced by protocols::analysis::PeptideDeriverFilter::derive_peptide(), protocols::analysis::PeptideDeriverFilter::prepare_pose(), protocols::analysis::PeptideDeriverFilter::report(), and protocols::analysis::InterfaceAnalyzerMover::set_use_tracer().

std::ostream& protocols::analysis::which_ostream	(	std::ostream &	ost,
		std::ostream &	oss,
		bool const	tracer
	)

stupid helper function needed because ternary operator does not allow variable return types

Referenced by protocols::analysis::LoopAnalyzerMover::apply(), protocols::analysis::InterfaceAnalyzerMover::print_pymol_selection_of_hbond_unsat(), and protocols::analysis::InterfaceAnalyzerMover::print_pymol_selection_of_interface_residues().