All Superinterfaces:

ChainNumberICode, Comparable<ChainNumberICode>, Serializable

All Known Implementing Classes:

DefaultPdbResidue, ImmutableDefaultPdbResidue
```
public interface PdbResidue
extends ChainNumberICode
```
A residue (nucleotide or amino acid).

Method Summary

All Methods Instance Methods Abstract Methods Default Methods
Modifier and Type	Method	Description
`default Set<AtomName>`	`atomNames()`
`List<PdbAtomLine>`	`atoms()`
`default String`	`chainIdentifier()`
`default PdbAtomLine`	`findAtom(AtomName atomName)`	Finds an atom of a given name.
`default boolean`	`hasAllHeavyAtoms()`	Compares the set of actual atoms in this residue with the set of expected atoms derived from the detected type of residue.
`default boolean`	`hasAnyHydrogen()`
`default boolean`	`hasAtom(AtomName atomName)`	Checks whether this residue has atom of the given name.
`PdbResidueIdentifier`	`identifier()`
`default String`	`insertionCode()`
`default boolean`	`isConnectedTo(PdbResidue other)`	Checks if this residue is connected with another one (see `MoleculeType.areConnected(PdbResidue, PdbResidue)`).
`default boolean`	`isMissing()`
`default boolean`	`isModified()`
`String`	`modifiedResidueName()`
`default PdbNamedResidueIdentifier`	`namedResidueIdentifier()`
`default org.apache.commons.math3.geometry.euclidean.threed.Plane`	`nucleobasePlane()`	Calculates the plane equation of the nucleobase in this residue.
`default char`	`oneLetterName()`
`default ResidueInformationProvider`	`residueInformationProvider()`	Detects the type of residue by its name and atom content.
`default int`	`residueNumber()`
`String`	`standardResidueName()`
`default String`	`toCif()`
`default String`	`toPdb()`

Methods inherited from interface pl.poznan.put.pdb.ChainNumberICode
compareTo

- Method Detail
  - identifier
```
PdbResidueIdentifier identifier()
```
    Returns:
    
    The identifier of a residue.
  - standardResidueName
```
String standardResidueName()
```
    Returns:
    
    The usual name of the residue. For example, a pseudouridine will be seen as uracil here.
  - modifiedResidueName
```
String modifiedResidueName()
```
    Returns:
    
    The name of the residue as read from PDB or mmCIF file.
  - atoms
```
List<PdbAtomLine> atoms()
```
    Returns:
    
    The list of atoms.
  - toPdb
```
default String toPdb()
```
    Returns:
    
    A text representation of this residue in PDB format.
  - toCif
```
default String toCif()
```
    Returns:
    
    A text representation of this residue in mmCIF format.
  - isMissing
```
default boolean isMissing()
```
    Returns:
    
    True if the list of atoms is empty.
  - residueInformationProvider
```
default ResidueInformationProvider residueInformationProvider()
```
    Detects the type of residue by its name and atom content.
    
    Returns:
    
    An instance with details about what this reside represents.
  - oneLetterName
```
default char oneLetterName()
```
    Returns:
    
    A one letter name which is lowercase for modified residues and uppercase otherwise.
  - isConnectedTo
```
default boolean isConnectedTo(PdbResidue other)
```
    Checks if this residue is connected with another one (see MoleculeType.areConnected(PdbResidue, PdbResidue)).
    
    Parameters:
    
    other - The other residue.
    
    Returns:
    
    True if this residue and the other one are connected.
  - chainIdentifier
```
default String chainIdentifier()
```
    Specified by:
    
    chainIdentifier in interface ChainNumberICode
    
    Returns:
    
    The identifier of the chain a residue belongs to.
  - residueNumber
```
default int residueNumber()
```
    Specified by:
    
    residueNumber in interface ChainNumberICode
    
    Returns:
    
    The number of a residue in the chain.
  - insertionCode
```
default String insertionCode()
```
    Specified by:
    
    insertionCode in interface ChainNumberICode
    
    Returns:
    
    Optional insertion code, used in some PDB and mmCIF files to represent "inserted" residues while maintaining the original numbering.
  - findAtom
```
default PdbAtomLine findAtom(AtomName atomName)
```
    Finds an atom of a given name.
    
    Parameters:
    
    atomName - An atom name.
    
    Returns:
    
    An instance of atom (with coordinates) of the given type.
  - nucleobasePlane
```
default org.apache.commons.math3.geometry.euclidean.threed.Plane nucleobasePlane()
```
    Calculates the plane equation of the nucleobase in this residue. This method works only for nucleotides and will throw an IllegalArgumentException for amino acids. The plane for purines (A or G) is based on N9, C2 and C6 atoms. The plane for pyrimidines (C, U or T) is based on N1, N3 and C5 atoms.
    
    Returns:
    
    The plane of the nucleobase.
  - namedResidueIdentifier
```
default PdbNamedResidueIdentifier namedResidueIdentifier()
```
    Returns:
    
    The instance of named identifier.
  - atomNames
```
default Set<AtomName> atomNames()
```
    Returns:
    
    The set of all atom names available in this residue.
  - hasAtom
```
default boolean hasAtom(AtomName atomName)
```
    Checks whether this residue has atom of the given name.
    
    Parameters:
    
    atomName - The atom name.
    
    Returns:
    
    True if this residue has an atom of the given name.
  - hasAnyHydrogen
```
default boolean hasAnyHydrogen()
```
    Returns:
    
    True if there is any hydrogen atom available in this residue.
  - hasAllHeavyAtoms
```
default boolean hasAllHeavyAtoms()
```
    Compares the set of actual atoms in this residue with the set of expected atoms derived from the detected type of residue.
    
    Returns:
    
    True if all expected heavy atoms (non-hydrogen) for this residue type are present in this residue.
  - isModified
```
default boolean isModified()
```
    Returns:
    
    True if the standard and modified residue names differ or if there are some atoms in the residue, but they do not match the expected set of atoms.

Interface PdbResidue

Method Summary

Methods inherited from interface pl.poznan.put.pdb.ChainNumberICode

Method Detail

identifier

standardResidueName

modifiedResidueName

atoms

toPdb

toCif

isMissing

residueInformationProvider

oneLetterName

isConnectedTo

chainIdentifier

residueNumber

insertionCode

findAtom

nucleobasePlane

namedResidueIdentifier

atomNames

hasAtom

hasAnyHydrogen

hasAllHeavyAtoms

isModified