Uses of Class
pl.poznan.put.pdb.PdbAtomLine

Packages that use PdbAtomLine

Package	Description
pl.poznan.put.pdb	Contains classes responsible for PDB/mmCIF data modelling and analysis.
pl.poznan.put.pdb.analysis	Contains classes which work on data from PDB or mmCIF files.
pl.poznan.put.rna
pl.poznan.put.torsion	Contains classes dealing with torsion angles handling.

Uses of PdbAtomLine in pl.poznan.put.pdb

Subclasses of PdbAtomLine in pl.poznan.put.pdb

Modifier and Type	Class	Description
class	ImmutablePdbAtomLine	Immutable implementation of PdbAtomLine.

Methods in pl.poznan.put.pdb that return PdbAtomLine

Modifier and Type	Method	Description
static PdbAtomLine	PdbAtomLine.fromBioJavaAtom(org.biojava.nbio.structure.Atom atom)	Creates an instance of this class from Atom object.
static PdbAtomLine	PdbAtomLine.parse(String line)	Parses text as ATOM or HETATM line in strict mode (all 80 characters in the line are required).
static PdbAtomLine	PdbAtomLine.parse(String line, boolean strictMode)	Parses text as ATOM or HETATM line in a strict or non-strict mode.

Methods in pl.poznan.put.pdb with parameters of type PdbAtomLine

Modifier and Type	Method	Description
static ImmutablePdbAtomLine	ImmutablePdbAtomLine.copyOf(PdbAtomLine instance)	Creates an immutable copy of a PdbAtomLine value.
double	PdbAtomLine.distanceTo(PdbAtomLine other)	Calculates the euclidean distance to another atom.
ImmutablePdbAtomLine.Builder	ImmutablePdbAtomLine.Builder.from(PdbAtomLine instance)	Fill a builder with attribute values from the provided pl.poznan.put.pdb.PdbAtomLine instance.

Uses of PdbAtomLine in pl.poznan.put.pdb.analysis

Methods in pl.poznan.put.pdb.analysis that return PdbAtomLine

Modifier and Type	Method	Description
default PdbAtomLine	PdbResidue.findAtom(AtomName atomName)	Finds an atom of a given name.

Methods in pl.poznan.put.pdb.analysis that return types with arguments of type PdbAtomLine

Modifier and Type	Method	Description
abstract List<PdbAtomLine>	DefaultCifModel.atoms()
abstract List<PdbAtomLine>	DefaultPdbModel.atoms()
abstract List<PdbAtomLine>	DefaultPdbResidue.atoms()
List<PdbAtomLine>	ImmutableDefaultCifModel.atoms()
List<PdbAtomLine>	ImmutableDefaultPdbModel.atoms()
List<PdbAtomLine>	ImmutableDefaultPdbResidue.atoms()
List<PdbAtomLine>	PdbModel.atoms()
List<PdbAtomLine>	PdbResidue.atoms()
default List<PdbAtomLine>	ResidueCollection.filteredAtoms(MoleculeType moleculeType)	Filters atoms in this residue collection.

Methods in pl.poznan.put.pdb.analysis with parameters of type PdbAtomLine

Modifier and Type	Method	Description
ImmutableDefaultCifModel.Builder	ImmutableDefaultCifModel.Builder.addAtoms(PdbAtomLine element)	Adds one element to atoms list.
ImmutableDefaultCifModel.Builder	ImmutableDefaultCifModel.Builder.addAtoms(PdbAtomLine... elements)	Adds elements to atoms list.
ImmutableDefaultPdbModel.Builder	ImmutableDefaultPdbModel.Builder.addAtoms(PdbAtomLine element)	Adds one element to atoms list.
ImmutableDefaultPdbModel.Builder	ImmutableDefaultPdbModel.Builder.addAtoms(PdbAtomLine... elements)	Adds elements to atoms list.
ImmutableDefaultPdbResidue.Builder	ImmutableDefaultPdbResidue.Builder.addAtoms(PdbAtomLine element)	Adds one element to atoms list.
ImmutableDefaultPdbResidue.Builder	ImmutableDefaultPdbResidue.Builder.addAtoms(PdbAtomLine... elements)	Adds elements to atoms list.
ImmutableDefaultCifModel	ImmutableDefaultCifModel.withAtoms(PdbAtomLine... elements)	Copy the current immutable object with elements that replace the content of atoms.
ImmutableDefaultPdbModel	ImmutableDefaultPdbModel.withAtoms(PdbAtomLine... elements)	Copy the current immutable object with elements that replace the content of atoms.
ImmutableDefaultPdbResidue	ImmutableDefaultPdbResidue.withAtoms(PdbAtomLine... elements)	Copy the current immutable object with elements that replace the content of atoms.

Method parameters in pl.poznan.put.pdb.analysis with type arguments of type PdbAtomLine

Modifier and Type	Method	Description
ImmutableDefaultCifModel.Builder	ImmutableDefaultCifModel.Builder.addAllAtoms(Iterable<? extends PdbAtomLine> elements)	Adds elements to atoms list.
ImmutableDefaultPdbModel.Builder	ImmutableDefaultPdbModel.Builder.addAllAtoms(Iterable<? extends PdbAtomLine> elements)	Adds elements to atoms list.
ImmutableDefaultPdbResidue.Builder	ImmutableDefaultPdbResidue.Builder.addAllAtoms(Iterable<? extends PdbAtomLine> elements)	Adds elements to atoms list.
ImmutableDefaultCifModel.Builder	ImmutableDefaultCifModel.Builder.atoms(Iterable<? extends PdbAtomLine> elements)	Sets or replaces all elements for atoms list.
ImmutableDefaultPdbModel.Builder	ImmutableDefaultPdbModel.Builder.atoms(Iterable<? extends PdbAtomLine> elements)	Sets or replaces all elements for atoms list.
ImmutableDefaultPdbResidue.Builder	ImmutableDefaultPdbResidue.Builder.atoms(Iterable<? extends PdbAtomLine> elements)	Sets or replaces all elements for atoms list.
static PdbModel	DefaultPdbModel.of(Iterable<PdbAtomLine> atoms)	Creates an instance of this class with just a list of atoms and all other fields set to default values or empty.
static ImmutableDefaultCifModel	ImmutableDefaultCifModel.of(PdbHeaderLine header, PdbExpdtaLine experimentalData, PdbRemark2Line resolution, int modelNumber, Iterable<? extends PdbAtomLine> atoms, Iterable<? extends PdbModresLine> modifiedResidues, Iterable<? extends PdbRemark465Line> missingResidues, String title, Iterable<? extends PdbResidueIdentifier> chainTerminatedAfter, Iterable<? extends QuantifiedBasePair> basePairs)	Construct a new immutable DefaultCifModel instance.
static ImmutableDefaultCifModel	ImmutableDefaultCifModel.of(PdbHeaderLine header, PdbExpdtaLine experimentalData, PdbRemark2Line resolution, int modelNumber, List<PdbAtomLine> atoms, List<PdbModresLine> modifiedResidues, List<PdbRemark465Line> missingResidues, String title, Set<PdbResidueIdentifier> chainTerminatedAfter, List<QuantifiedBasePair> basePairs)	Construct a new immutable DefaultCifModel instance.
static ImmutableDefaultPdbModel	ImmutableDefaultPdbModel.of(PdbHeaderLine header, PdbExpdtaLine experimentalData, PdbRemark2Line resolution, int modelNumber, Iterable<? extends PdbAtomLine> atoms, Iterable<? extends PdbModresLine> modifiedResidues, Iterable<? extends PdbRemark465Line> missingResidues, String title, Iterable<? extends PdbResidueIdentifier> chainTerminatedAfter)	Construct a new immutable DefaultPdbModel instance.
static ImmutableDefaultPdbModel	ImmutableDefaultPdbModel.of(PdbHeaderLine header, PdbExpdtaLine experimentalData, PdbRemark2Line resolution, int modelNumber, List<PdbAtomLine> atoms, List<PdbModresLine> modifiedResidues, List<PdbRemark465Line> missingResidues, String title, Set<PdbResidueIdentifier> chainTerminatedAfter)	Construct a new immutable DefaultPdbModel instance.
static ImmutableDefaultPdbResidue	ImmutableDefaultPdbResidue.of(PdbResidueIdentifier identifier, String standardResidueName, String modifiedResidueName, Iterable<? extends PdbAtomLine> atoms)	Construct a new immutable DefaultPdbResidue instance.
static ImmutableDefaultPdbResidue	ImmutableDefaultPdbResidue.of(PdbResidueIdentifier identifier, String standardResidueName, String modifiedResidueName, List<PdbAtomLine> atoms)	Construct a new immutable DefaultPdbResidue instance.
ImmutableDefaultCifModel	ImmutableDefaultCifModel.withAtoms(Iterable<? extends PdbAtomLine> elements)	Copy the current immutable object with elements that replace the content of atoms.
ImmutableDefaultPdbModel	ImmutableDefaultPdbModel.withAtoms(Iterable<? extends PdbAtomLine> elements)	Copy the current immutable object with elements that replace the content of atoms.
ImmutableDefaultPdbResidue	ImmutableDefaultPdbResidue.withAtoms(Iterable<? extends PdbAtomLine> elements)	Copy the current immutable object with elements that replace the content of atoms.

Uses of PdbAtomLine in pl.poznan.put.rna

Methods in pl.poznan.put.rna that return types with arguments of type PdbAtomLine

Modifier and Type	Method	Description
Optional<PdbAtomLine>	ImmutableStandardReferenceFrame.longAxisAtom()
Optional<PdbAtomLine>	StandardReferenceFrame.longAxisAtom()
default Map<AtomName,PdbAtomLine>	Nucleobase.standardReferenceFrame()

Method parameters in pl.poznan.put.rna with type arguments of type PdbAtomLine

Modifier and Type	Method	Description
ImmutableStandardReferenceFrame.Builder	ImmutableStandardReferenceFrame.Builder.longAxisAtom(Optional<PdbAtomLine> longAxisAtom)	Initializes the value for the longAxisAtom attribute.
ImmutableStandardReferenceFrame	ImmutableStandardReferenceFrame.withLongAxisAtom(Optional<PdbAtomLine> value)	Copy the current immutable object by setting a value for the longAxisAtom attribute.

Uses of PdbAtomLine in pl.poznan.put.torsion

Methods in pl.poznan.put.torsion with parameters of type PdbAtomLine

Modifier and Type	Method	Description
default TorsionAngleValue	AtomBasedTorsionAngleType.calculate(PdbAtomLine a1, PdbAtomLine a2, PdbAtomLine a3, PdbAtomLine a4)	Calculates a value of this torsion angle type given atoms explicitly.
ImmutableAtomPair.Builder	ImmutableAtomPair.Builder.leftAtom(PdbAtomLine leftAtom)	Initializes the value for the leftAtom attribute.
static ImmutableAtomPair	ImmutableAtomPair.of(PdbAtomLine leftAtom, PdbAtomLine rightAtom)	Construct a new immutable AtomPair instance.
ImmutableAtomPair.Builder	ImmutableAtomPair.Builder.rightAtom(PdbAtomLine rightAtom)	Initializes the value for the rightAtom attribute.
ImmutableAtomPair	ImmutableAtomPair.withLeftAtom(PdbAtomLine value)	Copy the current immutable object by setting a value for the leftAtom attribute.
ImmutableAtomPair	ImmutableAtomPair.withRightAtom(PdbAtomLine value)	Copy the current immutable object by setting a value for the rightAtom attribute.