Package pl.poznan.put.pdb.analysis
Contains classes which work on data from PDB or mmCIF files.
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Interface Summary Interface Description CifModel A structure parsed from an mmCIF file.ModelContainer A set of PDB files which all correspond to the same structure and also their chain names' mapping.PdbModel A structure parsed from a PDB file.PdbResidue A residue (nucleotide or amino acid).ResidueCollection A collection of residues.ResidueComponent A fragment of a residue with a set of expected atoms and a set of possible other atoms.ResidueInformationProvider A provider of detailed information about a residue (its type, expected atoms, torsion angles etc).SingleTypedResidueCollection A collection of residues with a common molecule type (RNA or protein). -
Class Summary Class Description AbstractPdbModel A structure which detects residues from atoms alone and then chains from residues.CifContainer A container of one or more PDB files converted from a single mmCIF file.CifConverter A converter from mmCIF to one or more PDB files.CifParser A parser of mmCIF format.DefaultCifModel A default implementation of a structure parsed from an mmCIF file.DefaultPdbModel A default implementation of a structure parsed from a PDB file.DefaultPdbResidue A default implementation of a residue (nucleotide or amino acid).DefaultResidueCollection A container for a list of residues.ImmutableCifContainer Immutable implementation ofCifContainer.ImmutableCifContainer.Builder Builds instances of typeImmutableCifContainer.ImmutableDefaultCifModel Immutable implementation ofDefaultCifModel.ImmutableDefaultCifModel.Builder Builds instances of typeImmutableDefaultCifModel.ImmutableDefaultPdbModel Immutable implementation ofDefaultPdbModel.ImmutableDefaultPdbModel.Builder Builds instances of typeImmutableDefaultPdbModel.ImmutableDefaultPdbResidue Immutable implementation ofDefaultPdbResidue.ImmutableDefaultPdbResidue.Builder Builds instances of typeImmutableDefaultPdbResidue.ImmutableDefaultResidueCollection Immutable implementation ofDefaultResidueCollection.ImmutableDefaultResidueCollection.Builder Builds instances of typeImmutableDefaultResidueCollection.ImmutablePdbChain Immutable implementation ofPdbChain.ImmutablePdbChain.Builder Builds instances of typeImmutablePdbChain.ImmutablePdbCompactFragment Immutable implementation ofPdbCompactFragment.ImmutablePdbCompactFragment.Builder Builds instances of typeImmutablePdbCompactFragment.ImmutableResidueTorsionAngles Immutable implementation ofResidueTorsionAngles.ImmutableResidueTorsionAngles.Builder Builds instances of typeImmutableResidueTorsionAngles.PdbChain A chain in a structure.PdbCompactFragment A collection of residues such that (i, i+1) are connected.PdbParser A parser of PDB format.ResidueTorsionAngles A collection of torsion angles values for a single residue.ResidueTypeDetector A detector of residue type based on its name and atom content. -
Enum Summary Enum Description MoleculeType A type of molecule (RNA or protein).