Strand (BioCommons 3.0.4 API)

All Superinterfaces:

DotBracket

All Known Implementing Classes:

DefaultStrand, ImmutableDefaultStrand, ImmutableStrandView, StrandView
```
public interface Strand
extends DotBracket
```
A continuous segment of residues. It might span the whole chain in PDB or just its fragments.

Method Summary

All Methods Instance Methods Abstract Methods Default Methods
Modifier and Type	Method	Description
`default int`	`begin()`
`default String`	`description()`	Prepares description of strand in RNAComposer format.
`default int`	`end()`
`default boolean`	`isSingleStrand()`	Checks if this strand is "single strand" which means that neither of its base pairs starts and ends in this strand.
`default TerminalMissing`	`missingBegin()`
`default TerminalMissing`	`missingEnd()`
`String`	`name()`
`default String`	`sequenceRY()`

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
  - name
```
String name()
```
    Returns:
    
    The name of the strand.
  - missingBegin
```
default TerminalMissing missingBegin()
```
    Returns:
    
    The missing residues at 5' end.
  - missingEnd
```
default TerminalMissing missingEnd()
```
    Returns:
    
    The missing residues at 3' end.
  - description
```
default String description()
```
    Prepares description of strand in RNAComposer format. The format has 5 elements: index-from, index-to, sequence, structure, RY-sequence.
    
    Returns:
    
    A description of strand in RNAComposer format.
  - begin
```
default int begin()
```
    Returns:
    
    The index of the first residue in this strand.
  - end
```
default int end()
```
    Returns:
    
    The index of the last residue in this strand.
  - isSingleStrand
```
default boolean isSingleStrand()
```
    Checks if this strand is "single strand" which means that neither of its base pairs starts and ends in this strand.
    
    Returns:
    
    True if there is no base-pair inside of this strand. An opening or closing bracket is allowed as long as it points somewhere outside this strand.
  - sequenceRY
```
default String sequenceRY()
```
    Returns:
    
    A sequence of R (instead of A and G) and Y (instead of C, U or T).