Package pl.poznan.put.structure.formats

Interface Strand

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

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

Method Details

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).