All Superinterfaces:

Serializable

All Known Subinterfaces:

CifModel, PdbModel, SingleTypedResidueCollection

All Known Implementing Classes:

AbstractPdbModel, DefaultCifModel, DefaultPdbModel, DefaultResidueCollection, ImmutableDefaultCifModel, ImmutableDefaultPdbModel, ImmutableDefaultResidueCollection, ImmutablePdbChain, ImmutablePdbCompactFragment, PdbChain, PdbCompactFragment

Functional Interface:

This is a functional interface and can therefore be used as the assignment target for a lambda expression or method reference.
```
@FunctionalInterface
public interface ResidueCollection
extends Serializable
```
A collection of residues.

Method Summary

All Methods Instance Methods Abstract Methods Default Methods
Modifier and Type	Method	Description
`default List<PdbAtomLine>`	`filteredAtoms(MoleculeType moleculeType)`	Filters atoms in this residue collection.
`default List<String>`	`findBondLengthViolations()`	Analyzes atomic bond lenths to find violations (too long or too short) and generates a report in a form of a list of validation messages.
`default PdbResidue`	`findResidue(ChainNumberICode query)`	Finds a residue by a triplet (chain, number, icode).
`default boolean`	`hasResidue(ChainNumberICode query)`	Checks if a given (chain, number, icode) is present in this collection of residues.
`default int`	`indexOf(ChainNumberICode query)`	Finds a residue by a triplet (chain, number, icode).
`default List<PdbNamedResidueIdentifier>`	`namedResidueIdentifiers()`
`default List<PdbResidueIdentifier>`	`residueIdentifiers()`
`List<PdbResidue>`	`residues()`
`default String`	`sequence()`	Generates a sequence out of this residue collection.
`default String`	`toCif()`	Generates a list of ATOM lines in mmCIF format from this instance.
`default String`	`toPdb()`	Generates a list of ATOM lines in PDB format from this instance.
`default ResidueCollection`	`withoutAlternateLocations()`	Creates a new instance of this class in which atoms with alternate locations are present only once.

- Method Detail
  - residues
```
List<PdbResidue> residues()
```
    Returns:
    
    The list of residues.
  - withoutAlternateLocations
```
default ResidueCollection withoutAlternateLocations()
```
    Creates a new instance of this class in which atoms with alternate locations are present only once.
    
    Returns:
    
    A copy of the current instance, but without alternate locations in atoms.
  - findBondLengthViolations
```
default List<String> findBondLengthViolations()
```
    Analyzes atomic bond lenths to find violations (too long or too short) and generates a report in a form of a list of validation messages.
    
    Returns:
    
    A list of error messages.
  - hasResidue
```
default boolean hasResidue(ChainNumberICode query)
```
    Checks if a given (chain, number, icode) is present in this collection of residues.
    
    Parameters:
    
    query - A residue identifier.
    
    Returns:
    
    True if a given residue is part of this collection.
  - findResidue
```
default PdbResidue findResidue(ChainNumberICode query)
```
    Finds a residue by a triplet (chain, number, icode).
    
    Parameters:
    
    query - A residue identifier.
    
    Returns:
    
    The residue found in this collection of residues.
  - indexOf
```
default int indexOf(ChainNumberICode query)
```
    Finds a residue by a triplet (chain, number, icode).
    
    Parameters:
    
    query - A residue identifier.
    
    Returns:
    
    The index of a residue found in this collection of residues.
  - sequence
```
default String sequence()
```
    Generates a sequence out of this residue collection.
    
    Returns:
    
    A sequence of one-letter-codes e.g. ACGGGG.
  - filteredAtoms
```
default List<PdbAtomLine> filteredAtoms(MoleculeType moleculeType)
```
    Filters atoms in this residue collection.
    
    Parameters:
    
    moleculeType - Type of molecule to leave in the result.
    
    Returns:
    
    A list of atoms of a given type.
  - residueIdentifiers
```
default List<PdbResidueIdentifier> residueIdentifiers()
```
    Returns:
    
    A list of residue identifiers.
  - namedResidueIdentifiers
```
default List<PdbNamedResidueIdentifier> namedResidueIdentifiers()
```
    Returns:
    
    A list of named residue identifiers.
  - toPdb
```
default String toPdb()
```
    Generates a list of ATOM lines in PDB format from this instance.
    
    Returns:
    
    A representation of this residue collection in PDB format.
  - toCif
```
default String toCif()
```
    Generates a list of ATOM lines in mmCIF format from this instance.
    
    Returns:
    
    A representation of this residue collection in mmCIF format.

Interface ResidueCollection

Method Summary

Method Detail

residues

withoutAlternateLocations

findBondLengthViolations

hasResidue

findResidue

indexOf

sequence

filteredAtoms

residueIdentifiers

namedResidueIdentifiers

toPdb

toCif