PdbCompactFragment (BioCommons 3.0.4 API)

java.lang.Object
- pl.poznan.put.pdb.analysis.PdbCompactFragment

All Implemented Interfaces:

Serializable, ResidueCollection, SingleTypedResidueCollection

Direct Known Subclasses:

ImmutablePdbCompactFragment
```
@Immutable
public abstract class PdbCompactFragment
extends Object
implements SingleTypedResidueCollection
```
A collection of residues such that (i, i+1) are connected.

See Also:

Serialized Form

Constructor Summary

Constructors
Constructor Description

PdbCompactFragment()

Method Summary

All Methods Instance Methods Abstract Methods Concrete Methods
Modifier and Type	Method	Description
`protected Set<TorsionAngleType>`	`angleTypes()`
`protected List<ResidueTorsionAngles>`	`angleValues()`
`String`	`name()`
`abstract List<PdbResidue>`	`residues()`
`PdbCompactFragment`	`shifted(int shift, int size)`	Creates a new instance from this one which starts from a shifted position and has a limited size.
`ResidueTorsionAngles`	`torsionAngles(PdbResidueIdentifier identifier)`	Computes torsion angles' values for a given residue.
`String`	`toString()`

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

Methods inherited from interface pl.poznan.put.pdb.analysis.ResidueCollection
filteredAtoms, findBondLengthViolations, findResidue, hasResidue, indexOf, namedResidueIdentifiers, residueIdentifiers, sequence, toCif, toPdb, withoutAlternateLocations

Methods inherited from interface pl.poznan.put.pdb.analysis.SingleTypedResidueCollection
moleculeType

- Constructor Detail
  - PdbCompactFragment
```
public PdbCompactFragment()
```
- Method Detail
  - residues
```
@Parameter(order=1)
public abstract List<PdbResidue> residues()
```
    Specified by:
    
    residues in interface ResidueCollection
    
    Returns:
    
    The list of residues.
  - name
```
@Default
public String name()
```
    Returns:
    
    The name of this compact fragment.
  - shifted
```
public final PdbCompactFragment shifted(int shift,
                                        int size)
```
    Creates a new instance from this one which starts from a shifted position and has a limited size.
    
    Parameters:
    
    shift - Starting position.
    
    size - Length of the new compact fragment.
    
    Returns:
    
    An instance of this class created by taking a sublist of the residues.
  - torsionAngles
```
public final ResidueTorsionAngles torsionAngles(PdbResidueIdentifier identifier)
```
    Computes torsion angles' values for a given residue.
    
    Parameters:
    
    identifier - A residue identifier.
    
    Returns:
    
    An object containing values of torsion angles in the given residue.
  - toString
```
public final String toString()
```
    Overrides:
    
    toString in class Object
  - angleTypes
```
@Lazy
protected Set<TorsionAngleType> angleTypes()
```
  - angleValues
```
@Lazy
protected List<ResidueTorsionAngles> angleValues()
```