ur_rna.StructureEditor.models

Class Motif.Helix

java.lang.Object

ur_rna.StructureEditor.models.Motif.Helix

All Implemented Interfaces:

java.lang.Iterable<Nuc>, IMotif, INucGroup

Enclosing class:

Motif

public static class Motif.Helix
extends java.lang.Object
implements IMotif

A helix represents a series of adjacent nucleotides which are all paired to a another series of adjacent nucleotides on the same RNA strand or a different RNA strand.

From this definition, it follows that a helix may be composed of either inter- or intra-molecular pairs but never both, and that a helix can include bases from at most two RNA strands.

Due to this definition, the only information required to store a helix unambiguously are the first and last bases of the series on either strand. Let these be called n5 and n3 (for the 5' and 3' bases respectively). It follows that n5 must belong to same strand as n3. Similarly n5.pairedTo must belong to the same strand as n3.pairedTo, but this is not necessarily the same strand that n5 and n3 belong to.

Field Summary

Fields

Modifier and Type	Field and Description
(package private) Nuc	nuc5 The 5'-most nucleotide in the helix.
(package private) int	pairCount The number of basepairs in the helix.

Constructor Summary

Constructors

Modifier	Constructor and Description
protected	Helix(Nuc nuc5, int pairCount)

Method Summary

Modifier and Type	Method and Description
private static boolean	bondIsNextInHelix(Bond prev, Bond current, ObjTools.RefInt orientation) Determines whether the "current" bond is immediately after the "prev" bond in a helix.
static java.util.List<Motif.Helix>	findAll(RnaScene scene) Find all distinct helices in specified list of strands.
Bond	first()
java.util.Collection<Nuc>	getBases() Get a set of all nucleotides included in the group.
static Motif.Helix	getHelix(Nuc nuc) Return the helix that contains the given nuc or null if nuc is not in a helix (ie.
Bond	getPair(int index)
RnaScene	getScene()
boolean	isClockwise()
protected static boolean	isHelixBond(Bond b)
boolean	isHybrid() Whether or not the helix contains inter-molecular pairs (i.e.
boolean	isParallel()
Bond	last()
Bond	lastPair()
int	size() Get the number of base-pairs in the helix (which is half the number of nucleotides).

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Methods inherited from interface ur_rna.StructureEditor.models.INucGroup

iterator, transformAll

Methods inherited from interface java.lang.Iterable

forEach, spliterator

Field Detail

nuc5

Nuc nuc5

The 5'-most nucleotide in the helix.

pairCount

int pairCount

The number of basepairs in the helix.

Constructor Detail

Helix

protected Helix(Nuc nuc5,
                int pairCount)

Method Detail

bondIsNextInHelix

private static boolean bondIsNextInHelix(Bond prev,
                                         Bond current,
                                         ObjTools.RefInt orientation)

Determines whether the "current" bond is immediately after the "prev" bond in a helix. Specifically: 1. current.type must be a valid helix bond (base pair) 2. The "from" nucleotides (current.nuc1 and prev.nuc1) must be on the same strand. 3. The "to" nucleotides (current.nuc2 and prev.nuc2) must be on the same strand (but not necessarily the same strand as nuc1) 4. The "from" nucleotide of current must be positioned immediately after that of "prev". (i.e. current.nuc1.index == prev.nuc1.index + 1) 5. The "to" nucleotide of current must be positioned immediately after OR before that of "prev". (i.e. current.nuc2.index == prev.nuc1.index +/- 1) (whether it is +1 or -1 will depend on the orientation of the second in the helix strand relative to the first.) 6. If the orientation of the second strand to the first is known (which will always be the case when at least two adjacent bonds have been identified) then the orientation between this bond and the last must match the one previously determined (e.g. from the preceding two bonds).

findAll

public static java.util.List<Motif.Helix> findAll(RnaScene scene)

Find all distinct helices in specified list of strands.

Returns:

a list of helices.

first

public Bond first()

getBases

public java.util.Collection<Nuc> getBases()

Description copied from interface: INucGroup

Get a set of all nucleotides included in the group.

Specified by:

getBases in interface INucGroup

Returns:

a Collection of nucleotides.

getHelix

public static Motif.Helix getHelix(Nuc nuc)

Return the helix that contains the given nuc or null if nuc is not in a helix (ie. it is unpaired)

getPair

public Bond getPair(int index)

getScene

public RnaScene getScene()

isClockwise

public boolean isClockwise()

isHelixBond

protected static boolean isHelixBond(Bond b)

isHybrid

public boolean isHybrid()

Whether or not the helix contains inter-molecular pairs (i.e. a hybridization of two distinct strands).

Returns:

true if n5.strand is different than n3.strand and false otherwise.

isParallel

public boolean isParallel()

last

public Bond last()

lastPair

public Bond lastPair()

size

public int size()

Get the number of base-pairs in the helix (which is half the number of nucleotides).

Returns:

The number of base-pairs in the helix.