protocols::peptide_deriver Namespace Reference

Classes
class	PeptideDeriverBasicStreamOutputter
	outputs a Peptiderive report to a stream in a basic, easily parsable format More...
class	CyclizedPeptideInfo
class	DerivedPeptideEntry
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...

Typedefs
typedef utility::pointer::shared_ptr< PeptideDeriverBasicStreamOutputter >	PeptideDeriverBasicStreamOutputterOP
typedef utility::pointer::shared_ptr< PeptideDeriverBasicStreamOutputter const >	PeptideDeriverBasicStreamOutputterCOP
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::shared_ptr< CyclizedPeptideInfo >	CyclizedPeptideInfoOP
typedef utility::pointer::shared_ptr< CyclizedPeptideInfo const >	CyclizedPeptideInfoCOP
typedef utility::pointer::shared_ptr< DerivedPeptideEntry >	DerivedPeptideEntryOP
typedef utility::pointer::shared_ptr< DerivedPeptideEntry const >	DerivedPeptideEntryCOP
typedef utility::pointer::shared_ptr< PeptideDeriverFilterCreator >	PeptideDeriverFilterCreatorOP
typedef utility::pointer::shared_ptr< PeptideDeriverFilterCreator const >	PeptideDeriverFilterCreatorCOP
typedef utility::pointer::shared_ptr< PeptideDeriverMarkdownStreamOutputter >	PeptideDeriverMarkdownStreamOutputterOP
typedef utility::pointer::shared_ptr< PeptideDeriverMarkdownStreamOutputter const >	PeptideDeriverMarkdownStreamOutputterCOP
typedef utility::pointer::shared_ptr< PeptideDeriverOutputterContainer >	PeptideDeriverOutputterContainerOP
typedef utility::pointer::shared_ptr< PeptideDeriverOutputterContainer const >	PeptideDeriverOutputterContainerCOP
typedef utility::pointer::shared_ptr< PeptideDeriverPoseOutputter >	PeptideDeriverPoseOutputterOP
typedef utility::pointer::shared_ptr< PeptideDeriverPoseOutputter const >	PeptideDeriverPoseOutputterCOP

Enumerations
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...
enum	CyclizationMethod { CYCLIZATION_METHOD_DISULFIDE =0 , CYCLIZATION_METHOD_END_TO_END , NUM_CYCLIZATION_METHODS }

Functions
static basic::Tracer	tracer ("protocols.peptide_deriver.PeptideDeriverFilter")

Variables
const std::string	CYCLIZATION_METHOD_NAMES [NUM_CYCLIZATION_METHODS] = { "disulfide", "end-to-end" }
const core::Real	UNLIKELY_ISC_VALUE = 2e6

Typedef Documentation

CyclizedPeptideInfoCOP

typedef utility::pointer::shared_ptr<CyclizedPeptideInfo const> protocols::peptide_deriver::CyclizedPeptideInfoCOP

CyclizedPeptideInfoOP

typedef utility::pointer::shared_ptr<CyclizedPeptideInfo> protocols::peptide_deriver::CyclizedPeptideInfoOP

DerivedPeptideEntryCOP

typedef utility::pointer::shared_ptr<DerivedPeptideEntry const> protocols::peptide_deriver::DerivedPeptideEntryCOP

DerivedPeptideEntryOP

typedef utility::pointer::shared_ptr<DerivedPeptideEntry> protocols::peptide_deriver::DerivedPeptideEntryOP

PeptideDeriverBasicStreamOutputterCOP

typedef utility::pointer::shared_ptr< PeptideDeriverBasicStreamOutputter const > protocols::peptide_deriver::PeptideDeriverBasicStreamOutputterCOP

PeptideDeriverBasicStreamOutputterOP

typedef utility::pointer::shared_ptr< PeptideDeriverBasicStreamOutputter > protocols::peptide_deriver::PeptideDeriverBasicStreamOutputterOP

PeptideDeriverFilterCOP

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

PeptideDeriverFilterCreatorCOP

typedef utility::pointer::shared_ptr< PeptideDeriverFilterCreator const > protocols::peptide_deriver::PeptideDeriverFilterCreatorCOP

PeptideDeriverFilterCreatorOP

typedef utility::pointer::shared_ptr< PeptideDeriverFilterCreator > protocols::peptide_deriver::PeptideDeriverFilterCreatorOP

PeptideDeriverFilterOP

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

PeptideDeriverMarkdownStreamOutputterCOP

typedef utility::pointer::shared_ptr< PeptideDeriverMarkdownStreamOutputter const > protocols::peptide_deriver::PeptideDeriverMarkdownStreamOutputterCOP

PeptideDeriverMarkdownStreamOutputterOP

typedef utility::pointer::shared_ptr< PeptideDeriverMarkdownStreamOutputter > protocols::peptide_deriver::PeptideDeriverMarkdownStreamOutputterOP

PeptideDeriverOutputterContainerCOP

typedef utility::pointer::shared_ptr< PeptideDeriverOutputterContainer const > protocols::peptide_deriver::PeptideDeriverOutputterContainerCOP

PeptideDeriverOutputterContainerOP

typedef utility::pointer::shared_ptr< PeptideDeriverOutputterContainer > protocols::peptide_deriver::PeptideDeriverOutputterContainerOP

PeptideDeriverOutputterCOP

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

PeptideDeriverOutputterOP

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

PeptideDeriverPoseOutputterCOP

typedef utility::pointer::shared_ptr< PeptideDeriverPoseOutputter const > protocols::peptide_deriver::PeptideDeriverPoseOutputterCOP

PeptideDeriverPoseOutputterOP

typedef utility::pointer::shared_ptr< PeptideDeriverPoseOutputter > protocols::peptide_deriver::PeptideDeriverPoseOutputterOP

Enumeration Type Documentation

CyclizationMethod

enum protocols::peptide_deriver::CyclizationMethod

Enumerator
CYCLIZATION_METHOD_DISULFIDE
CYCLIZATION_METHOD_END_TO_END
NUM_CYCLIZATION_METHODS

PeptideDeriverEntryType

enum protocols::peptide_deriver::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.

PeptideDeriverReportFormat

enum protocols::peptide_deriver::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

tracer()

static basic::Tracer protocols::peptide_deriver::tracer ( "protocols.peptide_deriver.PeptideDeriverFilter"  )

static

Referenced by protocols::peptide_deriver::PeptideDeriverFilter::derive_peptide(), protocols::peptide_deriver::PeptideDeriverFilter::prepare_pose(), and protocols::peptide_deriver::PeptideDeriverFilter::report().

Variable Documentation

CYCLIZATION_METHOD_NAMES

const std::string protocols::peptide_deriver::CYCLIZATION_METHOD_NAMES[NUM_CYCLIZATION_METHODS] = { "disulfide", "end-to-end" }

Referenced by protocols::peptide_deriver::PeptideDeriverMarkdownStreamOutputter::begin_structure(), and protocols::peptide_deriver::PeptideDeriverBasicStreamOutputter::peptide_entry().

UNLIKELY_ISC_VALUE

const core::Real protocols::peptide_deriver::UNLIKELY_ISC_VALUE = 2e6

Referenced by protocols::peptide_deriver::PeptideDeriverFilter::derive_peptide().