Uses of Interface
pl.poznan.put.pdb.analysis.PdbModel

Packages that use PdbModel

Package	Description
pl.poznan.put.pdb.analysis	Contains classes which work on data from PDB or mmCIF files.
pl.poznan.put.rna
pl.poznan.put.structure.formats

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

Subinterfaces of PdbModel in pl.poznan.put.pdb.analysis

Modifier and Type	Interface	Description
interface	CifModel	A structure parsed from an mmCIF file.

Classes in pl.poznan.put.pdb.analysis that implement PdbModel

Modifier and Type	Class	Description
class	AbstractPdbModel	A structure which detects residues from atoms alone and then chains from residues.
class	DefaultCifModel	A default implementation of a structure parsed from an mmCIF file.
class	DefaultPdbModel	A default implementation of a structure parsed from a PDB file.
class	ImmutableDefaultCifModel	Immutable implementation of DefaultCifModel.
class	ImmutableDefaultPdbModel	Immutable implementation of DefaultPdbModel.

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

Modifier and Type	Method	Description
PdbModel	DefaultPdbModel.filteredNewInstance(MoleculeType moleculeType)
PdbModel	PdbModel.filteredNewInstance(MoleculeType moleculeType)	Filters out residues of a given molecule type (RNA or protein) and creates a new instance of this class.
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.

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

Modifier and Type	Method	Description
List<PdbModel>	PdbParser.parse(String structureContent)	Parses a string in PDB format.

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

Modifier and Type	Method	Description
ImmutableDefaultCifModel.Builder	ImmutableDefaultCifModel.Builder.from(PdbModel instance)	Fill a builder with attribute values from the provided pl.poznan.put.pdb.analysis.PdbModel instance.
ImmutableDefaultPdbModel.Builder	ImmutableDefaultPdbModel.Builder.from(PdbModel instance)	Fill a builder with attribute values from the provided pl.poznan.put.pdb.analysis.PdbModel instance.

Uses of PdbModel in pl.poznan.put.rna

Methods in pl.poznan.put.rna that return PdbModel

Modifier and Type	Method	Description
static PdbModel	ChainReorderer.reorderAtoms(PdbModel model)	Finds canonical base pairs (see CanonicalStructureExtractor.basePairs(ResidueCollection)) and reorders chains to keep connected ones together while minimizing the overall pseudoknot order.
static PdbModel	ChainReorderer.reorderAtoms(PdbModel model, Collection<? extends ClassifiedBasePair> basePairs)	Reorders chains according to given canonical base pairs to keep connected chains together while minimizing the overall pseudoknot order.

Methods in pl.poznan.put.rna with parameters of type PdbModel

Modifier and Type	Method	Description
static PdbModel	ChainReorderer.reorderAtoms(PdbModel model)	Finds canonical base pairs (see CanonicalStructureExtractor.basePairs(ResidueCollection)) and reorders chains to keep connected ones together while minimizing the overall pseudoknot order.
static PdbModel	ChainReorderer.reorderAtoms(PdbModel model, Collection<? extends ClassifiedBasePair> basePairs)	Reorders chains according to given canonical base pairs to keep connected chains together while minimizing the overall pseudoknot order.

Uses of PdbModel in pl.poznan.put.structure.formats

Methods in pl.poznan.put.structure.formats that return PdbModel

Modifier and Type	Method	Description
abstract PdbModel	DefaultDotBracketFromPdb.model()
PdbModel	ImmutableDefaultDotBracketFromPdb.model()

Methods in pl.poznan.put.structure.formats with parameters of type PdbModel

Modifier and Type	Method	Description
static Ct	Ct.fromBpSeqAndPdbModel(BpSeq bpSeq, PdbModel model)	Converts RNA secondary structure in BPSEQ format to CT format, taking into account information from 3D coordinates (residue numbering, chain sizes).
static Ct.ExtendedEntry	Ct.ExtendedEntry.fromEntryAndPdbResidue(BpSeq.Entry entry, ChainNumberICode residue, PdbModel model)	Converts a BPSEQ entry into an instance of this class using information from a parsed 3D data.
ImmutableDefaultDotBracketFromPdb.Builder	ImmutableDefaultDotBracketFromPdb.Builder.model(PdbModel model)	Initializes the value for the model attribute.
static ImmutableDefaultDotBracketFromPdb	ImmutableDefaultDotBracketFromPdb.of(String sequence, String structure, PdbModel model)	Construct a new immutable DefaultDotBracketFromPdb instance.
ImmutableDefaultDotBracketFromPdb	ImmutableDefaultDotBracketFromPdb.withModel(PdbModel value)	Copy the current immutable object by setting a value for the model attribute.