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
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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.