Package pl.poznan.put.pdb.analysis

Class ImmutableDefaultPdbResidue

java.lang.Object

pl.poznan.put.pdb.analysis.DefaultPdbResidue

pl.poznan.put.pdb.analysis.ImmutableDefaultPdbResidue

All Implemented Interfaces:

Serializable, Comparable<ChainNumberICode>, PdbResidue, ChainNumberICode

@ParametersAreNonnullByDefault
@Generated("org.immutables.processor.ProxyProcessor")
@Immutable
public final class ImmutableDefaultPdbResidue
extends DefaultPdbResidue

Immutable implementation of DefaultPdbResidue.

Use the builder to create immutable instances: ImmutableDefaultPdbResidue.builder(). Use the static factory method to create immutable instances: ImmutableDefaultPdbResidue.of().

See Also:

Serialized Form

Nested Class Summary

Nested Classes

Modifier and Type	Class	Description
static class	ImmutableDefaultPdbResidue.Builder	Builds instances of type ImmutableDefaultPdbResidue.

Method Summary

Modifier and Type	Method	Description
Set<AtomName>	atomNames()
List<PdbAtomLine>	atoms()
static ImmutableDefaultPdbResidue.Builder	builder()	Creates a builder for ImmutableDefaultPdbResidue.
static ImmutableDefaultPdbResidue	copyOf(DefaultPdbResidue instance)	Creates an immutable copy of a DefaultPdbResidue value.
boolean	equals(Object another)	This instance is equal to all instances of ImmutableDefaultPdbResidue that have equal attribute values.
boolean	hasAllHeavyAtoms()	Compares the set of actual atoms in this residue with the set of expected atoms derived from the detected type of residue.
int	hashCode()	Computes a hash code from attributes: identifier, standardResidueName, modifiedResidueName, atoms.
PdbResidueIdentifier	identifier()
String	modifiedResidueName()
static ImmutableDefaultPdbResidue	of(PdbResidueIdentifier identifier, String standardResidueName, String modifiedResidueName, Iterable<? extends PdbAtomLine> atoms)	Construct a new immutable DefaultPdbResidue instance.
static ImmutableDefaultPdbResidue	of(PdbResidueIdentifier identifier, String standardResidueName, String modifiedResidueName, List<PdbAtomLine> atoms)	Construct a new immutable DefaultPdbResidue instance.
ResidueInformationProvider	residueInformationProvider()	Detects the type of residue by its name and atom content.
String	standardResidueName()
ImmutableDefaultPdbResidue	withAtoms(Iterable<? extends PdbAtomLine> elements)	Copy the current immutable object with elements that replace the content of atoms.
ImmutableDefaultPdbResidue	withAtoms(PdbAtomLine... elements)	Copy the current immutable object with elements that replace the content of atoms.
ImmutableDefaultPdbResidue	withIdentifier(PdbResidueIdentifier value)	Copy the current immutable object by setting a value for the identifier attribute.
ImmutableDefaultPdbResidue	withModifiedResidueName(String value)	Copy the current immutable object by setting a value for the modifiedResidueName attribute.
ImmutableDefaultPdbResidue	withStandardResidueName(String value)	Copy the current immutable object by setting a value for the standardResidueName attribute.

Methods inherited from class pl.poznan.put.pdb.analysis.DefaultPdbResidue

fromBioJavaGroup, toString

Methods inherited from class java.lang.Object

clone, finalize, getClass, notify, notifyAll, wait, wait, wait

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

compareTo

Methods inherited from interface pl.poznan.put.pdb.analysis.PdbResidue

chainIdentifier, findAtom, hasAnyHydrogen, hasAtom, insertionCode, isConnectedTo, isMissing, isModified, namedResidueIdentifier, nucleobasePlane, oneLetterName, residueNumber, toCif, toPdb

Method Detail

identifier

public PdbResidueIdentifier identifier()

Specified by:

identifier in interface PdbResidue

Specified by:

identifier in class DefaultPdbResidue

Returns:

The value of the identifier attribute

standardResidueName

public String standardResidueName()

Specified by:

standardResidueName in interface PdbResidue

Specified by:

standardResidueName in class DefaultPdbResidue

Returns:

The value of the standardResidueName attribute

modifiedResidueName

public String modifiedResidueName()

Specified by:

modifiedResidueName in interface PdbResidue

Specified by:

modifiedResidueName in class DefaultPdbResidue

Returns:

The value of the modifiedResidueName attribute

atoms

public List<PdbAtomLine> atoms()

Specified by:

atoms in interface PdbResidue

Specified by:

atoms in class DefaultPdbResidue

Returns:

The value of the atoms attribute

withIdentifier

public final ImmutableDefaultPdbResidue withIdentifier(PdbResidueIdentifier value)

Copy the current immutable object by setting a value for the identifier attribute. A shallow reference equality check is used to prevent copying of the same value by returning this.

Parameters:

value - A new value for identifier

Returns:

A modified copy of the this object

withStandardResidueName

public final ImmutableDefaultPdbResidue withStandardResidueName(String value)

Copy the current immutable object by setting a value for the standardResidueName attribute. An equals check used to prevent copying of the same value by returning this.

Parameters:

value - A new value for standardResidueName

Returns:

A modified copy of the this object

withModifiedResidueName

public final ImmutableDefaultPdbResidue withModifiedResidueName(String value)

Copy the current immutable object by setting a value for the modifiedResidueName attribute. An equals check used to prevent copying of the same value by returning this.

Parameters:

value - A new value for modifiedResidueName

Returns:

A modified copy of the this object

withAtoms

public final ImmutableDefaultPdbResidue withAtoms(PdbAtomLine... elements)

Copy the current immutable object with elements that replace the content of atoms.

Parameters:

elements - The elements to set

Returns:

A modified copy of this object

withAtoms

public final ImmutableDefaultPdbResidue withAtoms(Iterable<? extends PdbAtomLine> elements)

Copy the current immutable object with elements that replace the content of atoms. A shallow reference equality check is used to prevent copying of the same value by returning this.

Parameters:

elements - An iterable of atoms elements to set

Returns:

A modified copy of this object

equals

public boolean equals(@Nullable
                      Object another)

This instance is equal to all instances of ImmutableDefaultPdbResidue that have equal attribute values.

Overrides:

equals in class Object

Returns:

true if this is equal to another instance

hashCode

public int hashCode()

Computes a hash code from attributes: identifier, standardResidueName, modifiedResidueName, atoms.

Overrides:

hashCode in class Object

Returns:

hashCode value

residueInformationProvider

public ResidueInformationProvider residueInformationProvider()

Detects the type of residue by its name and atom content.

Returns a lazily initialized value of the residueInformationProvider attribute. Initialized once and only once and stored for subsequent access with proper synchronization. In case of any exception or error thrown by the lazy value initializer, the result will not be memoised (i.e. remembered) and on next call computation will be attempted again.

Specified by:

residueInformationProvider in interface PdbResidue

Overrides:

residueInformationProvider in class DefaultPdbResidue

Returns:

A lazily initialized value of the residueInformationProvider attribute

atomNames

public Set<AtomName> atomNames()

Returns a lazily initialized value of the atomNames attribute. Initialized once and only once and stored for subsequent access with proper synchronization. In case of any exception or error thrown by the lazy value initializer, the result will not be memoised (i.e. remembered) and on next call computation will be attempted again.

Specified by:

atomNames in interface PdbResidue

Overrides:

atomNames in class DefaultPdbResidue

Returns:

A lazily initialized value of the atomNames attribute

hasAllHeavyAtoms

public 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 a lazily initialized value of the hasAllHeavyAtoms attribute. Initialized once and only once and stored for subsequent access with proper synchronization. In case of any exception or error thrown by the lazy value initializer, the result will not be memoised (i.e. remembered) and on next call computation will be attempted again.

Specified by:

hasAllHeavyAtoms in interface PdbResidue

Overrides:

hasAllHeavyAtoms in class DefaultPdbResidue

Returns:

A lazily initialized value of the hasAllHeavyAtoms attribute

of

public static ImmutableDefaultPdbResidue of(PdbResidueIdentifier identifier,
                                            String standardResidueName,
                                            String modifiedResidueName,
                                            List<PdbAtomLine> atoms)

Construct a new immutable DefaultPdbResidue instance.

Parameters:

identifier - The value for the identifier attribute

standardResidueName - The value for the standardResidueName attribute

modifiedResidueName - The value for the modifiedResidueName attribute

atoms - The value for the atoms attribute

Returns:

An immutable DefaultPdbResidue instance

of

public static ImmutableDefaultPdbResidue of(PdbResidueIdentifier identifier,
                                            String standardResidueName,
                                            String modifiedResidueName,
                                            Iterable<? extends PdbAtomLine> atoms)

Construct a new immutable DefaultPdbResidue instance.

Parameters:

identifier - The value for the identifier attribute

standardResidueName - The value for the standardResidueName attribute

modifiedResidueName - The value for the modifiedResidueName attribute

atoms - The value for the atoms attribute

Returns:

An immutable DefaultPdbResidue instance

copyOf

public static ImmutableDefaultPdbResidue copyOf(DefaultPdbResidue instance)

Creates an immutable copy of a DefaultPdbResidue value. Uses accessors to get values to initialize the new immutable instance. If an instance is already immutable, it is returned as is.

Parameters:

instance - The instance to copy

Returns:

A copied immutable DefaultPdbResidue instance

builder

public static ImmutableDefaultPdbResidue.Builder builder()

Creates a builder for ImmutableDefaultPdbResidue.

 ImmutableDefaultPdbResidue.builder()
    .identifier(pl.poznan.put.pdb.PdbResidueIdentifier) // required identifier
    .standardResidueName(String) // required standardResidueName
    .modifiedResidueName(String) // required modifiedResidueName
    .addAtoms|addAllAtoms(pl.poznan.put.pdb.PdbAtomLine) // atoms elements
    .build();
 

Returns:

A new ImmutableDefaultPdbResidue builder