DotBracketFromPdb (BioCommons 3.0.4 API)

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

All Methods Instance Methods Abstract Methods
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, length, missingInternal, missingTerminal, originalIndex, pairs, pseudoknotOrder, sequence, sequence, strands, structure, structure, symbols, toStringWithStrands

- Method Detail
  - 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.