BasePair (BioCommons 3.0.4 API)

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

All Methods Static Methods Instance Methods Abstract Methods Concrete Methods
Modifier and Type	Method	Description
`int`	`compareTo(BasePair t)`
`BasePair`	`invert()`
`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()`
`String`	`toString()`

Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

- Constructor Detail
  - BasePair
```
public BasePair()
```
- Method Detail
  - 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>