Biological data structures¶
For crystals created from the Protein Data Bank, the atoms will be stored in substructures. These substructures are described below.
Primary Structure: Residues¶
- class crystals.Residue(atoms: AtomicStructure, name: str, sequence_number: int, **kwargs)¶
Bases:
AtomicStructure
Fundamental building block of a protein: amino acid residue.
- Parameters
atoms (iterable, optional) – Atoms not attached to a substructure.
name (str) – Residue name, e.g. “GLY”
sequence_number (int) – Sequence number within a protein.
Secondary Structure¶
Secondary structures are really all the same, with different names:
- class crystals.biological.SecondaryStructure(residues: Iterable[Residue], sequence_number: int, **kwargs)¶
Bases:
AtomicStructure
Abstract container representing protein secondary structures (i.e. helices, sheets, etc.)
- Parameters
residues (iterable, optional) – Residues making this structure.
sequence_number (int) – Sequence number within a protein.
Helix¶
- class crystals.Helix(residues: Iterable[Residue], sequence_number: int, **kwargs)¶
Bases:
SecondaryStructure
Container representing a protein helix.
- Parameters
residues (iterable, optional) – Residues making this helix.
sequence_number (int) – Sequence number within a protein.
Sheet¶
- class crystals.Sheet(residues: Iterable[Residue], sequence_number: int, **kwargs)¶
Bases:
SecondaryStructure
Container representing a protein sheet.
- Parameters
residues (iterable, optional) – Residues making this sheet.
sequence_number (int) – Sequence number within a protein.