Rosetta  2021.16
 All Classes Namespaces Files Functions Variables Typedefs Enumerations Enumerator Friends Macros Pages
Classes | Typedefs | Enumerations | Functions | Variables
protocols::peptide_deriver Namespace Reference

Classes

class  CyclizedPeptideInfo
 
class  DerivedPeptideEntry
 
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...
 

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

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

Enumeration Type Documentation

Enumerator
CYCLIZATION_METHOD_DISULFIDE 
CYCLIZATION_METHOD_END_TO_END 
NUM_CYCLIZATION_METHODS 

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.

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

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

Variable Documentation

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