Package csb :: Package bio :: Package structure

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# Package structure

source code

3D and secondary structure APIs.

This module defines some of the most fundamental abstractions in the library: Structure, Chain, Residue and Atom. Instances of these objects may exist independently and that is perfectly fine, but usually they are part of a Composite aggregation. The root node in this Composite is a Structure (or Ensemble). Structures are composed of Chains, and each Chain is a collection of Residues. The leaf node is Atom.

All of these objects implement the base AbstractEntity interface. Therefore, every node in the Composite can be transformed:

    >>> r, t = [rotation matrix], [translation vector]
    >>> entity.transform(r, t)

and it knows its immediate children:

    >>> entity.items
    <iterator>    # over all immediate child entities

If you want to traverse the complete Composite tree, starting at arbitrary level, and down to the lowest level, use one of the CompositeEntityIterators. Or just call AbstractEntity.components:

    >>> entity.components()
    <iterator>   # over all descendants, of any type, at any level
    >>> entity.components(klass=Residue)
    <iterator>   # over all Residue descendants

Some of the inner objects in this hierarchy behave just like dictionaries (but are not):

    >>> structure.chains['A']       # access chain A by ID
    <Chain A: Protein>
    >>> structure['A']              # the same
    <Chain A: Protein>
    >>> residue.atoms['CS']
    <Atom: CA>                      # access an atom by its name
    >>> residue.atoms['CS']
    <Atom: CA>                      # the same

Others behave like list collections:

    >>> chain.residues[10]               # 1-based access to the residues in the chain
    <ProteinResidue [10]: PRO 10>
    >>> chain[10]                        # 0-based, list-like access
    <ProteinResidue [11]: GLY 11>

Step-wise building of Ensembles, Chains and Residues is supported through a number of `append` methods, for example:

    >>> residue = ProteinResidue(401, ProteinAlphabet.ALA)
    >>> s.chains['A'].residues.append(residue)

See EnsembleModelsCollection, StructureChainsTable, ChainResiduesCollection and ResidueAtomsTable for more details.

Some other objects in this module of potential interest are the self-explanatory SecondaryStructure and TorsionAngles.

Classes
| AbstractEntity Base class for all protein structure entities.
| AlignmentArgumentLengthError
| AngleUnits Torsion angle unit types
| Atom Represents a single atom in space.
| AtomNotFoundError
| Broken3DStructureError
| BrokenSecStructureError
| Chain Represents a polymeric chain.
| ChainNotFoundError
| ChainResiduesCollection
| ChemElements Periodic table elements
| CompositeEntityIterator Iterates over composite AbstractEntity hierarchies.
| ConfinedEntityIterator Iterates over composite AbstractEntity hierarchies, but terminates the traversal of a branch once a specific node type is encountered.
| DisorderedAtom A wobbling atom, which has alternative locations.
| DuplicateAtomIDError
| DuplicateChainIDError
| DuplicateModelIDError
| DuplicateResidueIDError
| Ensemble Represents an ensemble of multiple Structure models.
| EnsembleModelsCollection
| EntityIndexError
| EntityNotFoundError
| InvalidOperation
| Missing3DStructureError
| NucleicResidue Represents a single nucleotide residue.
| ProteinResidue Represents a single amino acid residue.
| Residue Base class representing a single residue.
| ResidueAtomsTable Represents a collection of atoms.
| SecStructures Secondary structure types
| SecondaryStructure Describes the secondary structure of a chain.
| SecondaryStructureElement Describes a Secondary Structure Element.
| Structure Represents a single model of a PDB 3-Dimensional molecular structure.
| StructureChainsTable
| SuperimposeInfo Describes a structural alignment result.
| TorsionAngles Describes a collection of phi, psi and omega backbone torsion angles.
| TorsionAnglesCollection Describes a collection of torsion angles.
| UnknownResidue
| UnknownSecStructureError

Variables
| __package__ = ``'``csb.bio.structure``'``