Package pl.poznan.put.structure.formats

Interface DotBracketFromPdb

All Superinterfaces:

DotBracket

All Known Implementing Classes:

CombinedStrandFromPdb, DefaultDotBracketFromPdb, ImmutableCombinedStrandFromPdb, ImmutableDefaultDotBracketFromPdb

public interface DotBracketFromPdb
extends DotBracket

A dot-bracket structure with correspondence to a 3D structure.

Method Summary

Modifier and Type	Method	Description
List<DotBracketFromPdb>	combineStrands(List<ClassifiedBasePair> nonCanonical)	Combines strands which are connected via canonical or non-canonical base pairs.
boolean	contains(PdbResidueIdentifier residueIdentifier)	Checks if this structure contains a mapping for the given residue identifier.
PdbResidueIdentifier	identifier(DotBracketSymbol symbol)	Maps the given dot-bracket symbol to its corresponding residue identifier.
Set<PdbResidueIdentifier>	identifierSet()
DotBracketSymbol	symbol(PdbResidueIdentifier residueIdentifier)	Maps the given residue identifier to its corresponding dot-bracket symbol.

Methods inherited from interface pl.poznan.put.structure.formats.DotBracket

combineStrands, containsMissing, findStrand, isIsolated, isolatedSymbols, length, missingInternal, missingTerminal, originalIndex, pairs, pseudoknotOrder, sequence, sequence, strands, structure, structure, symbols, toStringWithStrands

Method Details

identifier

PdbResidueIdentifier identifier(DotBracketSymbol symbol)

Maps the given dot-bracket symbol to its corresponding residue identifier.

Parameters:

symbol - The symbol to look for.

Returns:

The PDB residue identifier.

symbol

DotBracketSymbol symbol(PdbResidueIdentifier residueIdentifier)

Maps the given residue identifier to its corresponding dot-bracket symbol.

Parameters:

residueIdentifier - The residue identifier to look for.

Returns:

The dot-bracket symbol.

contains

boolean contains(PdbResidueIdentifier residueIdentifier)

Checks if this structure contains a mapping for the given residue identifier.

Parameters:

residueIdentifier - The residue identifier to check.

Returns:

True, if there is a mapping for the given residue identifier.

combineStrands

List<DotBracketFromPdb> combineStrands(List<ClassifiedBasePair> nonCanonical)

Combines strands which are connected via canonical or non-canonical base pairs.

Parameters:

nonCanonical - The list of non-canonical base pairs to take into account.

Returns:

The list of dot-bracket structures from the combined strands.

identifierSet

Set<PdbResidueIdentifier> identifierSet()

Returns:

The set of residue identifiers used in this structure.