Package pl.poznan.put.structure

Class BasePair

java.lang.Object

pl.poznan.put.structure.BasePair

All Implemented Interfaces:

Serializable, Comparable<BasePair>

Direct Known Subclasses:

ImmutableBasePair

@Immutable
public abstract class BasePair
extends Object
implements Serializable, Comparable<BasePair>

A pairing between two nucleotides' bases.

See Also:

• Serialized Form

Constructor Summary

Constructors

Constructor	Description
BasePair()

Method Summary

Modifier and Type	Method	Description
final int	compareTo(BasePair t)
final BasePair	invert()
final boolean	is5to3()
static boolean	isCanonicalPair(PdbResidue left, PdbResidue right)	Checks if two residues are canonical base pairs by means of (1) distance between atoms which form hydrogen bonds and (2) checking if two bases face each other.
abstract PdbNamedResidueIdentifier	left()
abstract PdbNamedResidueIdentifier	right()
final String	toString()

Methods inherited from class java.lang.Object

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

Constructor Details

BasePair

public BasePair()

Method Details

isCanonicalPair

public static boolean isCanonicalPair(PdbResidue left,
 PdbResidue right)

Checks if two residues are canonical base pairs by means of (1) distance between atoms which form hydrogen bonds and (2) checking if two bases face each other.

Parameters:

left - First residue.

right - Second residue.

Returns:

True if there is a pair of C-G, A-U or G-U.

left

@Parameter(order=1)
public abstract PdbNamedResidueIdentifier left()

Returns:

The first residue.

right

@Parameter(order=2)
public abstract PdbNamedResidueIdentifier right()

Returns:

The second residue.

invert

public final BasePair invert()

is5to3

public final boolean is5to3()

Returns:

True if the first residue is before the second one in 5'-3' order.

toString

public final String toString()

Overrides:

toString in class Object

compareTo

public final int compareTo(BasePair t)

Specified by:

compareTo in interface Comparable<BasePair>