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, name, sequence_number, **kwargs)

Bases: crystals.base.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, sequence_number, **kwargs)

Bases: crystals.base.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, sequence_number, **kwargs)

Bases: crystals.biological.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, sequence_number, **kwargs)

Bases: crystals.biological.SecondaryStructure

Container representing a protein sheet.

Parameters
  • residues (iterable, optional) – Residues making this sheet.

  • sequence_number (int) – Sequence number within a protein.