atomium.data

Contains logic for turning data dictionaies into a parsed Python objects.

class atomium.data.File(filetype)[source]

When a file is parsed, the result is a File. It contains the structure of interest, as well as meta information.

Parameters

filetype (str) – the type of file that was parsed to make this.

property assemblies

The structure’s biological assembly instructions.

Return type

list

property authors

The structure’s authors.

Return type

list

property classification

The structure’s formal classification.

Return type

str

property code

The unique database identifer for this structure.

Return type

str

property deposition_date

The date the structure was submitted for publication.

Return type

datetime.date

property expression_system

The organism the structure was expressed in.

Return type

float

property filetype

The filetype that this File was created from, such as .pdb or .cif.

Return type

str

generate_assembly(id)[source]

Generates a new model from the existing model using one of the file’s set of assembly instructions (for which you provide the ID).

For example:

>>> import atomium
>>> pdb = atomium.fetch('1xda')
>>> pdb.model
<Model (8 chains, 16 ligands)>
>>> pdb.generate_assembly(1)
<Model (2 chains, 4 ligands)>
>>> pdb.generate_assembly(5)
<Model (12 chains, 24 ligands)>
Parameters

id (int) – the ID of the assembly to generate.

Return type

Model

property keywords

The structure’s keyword descriptors.

Return type

list

property missing_residues

The residues that should be in the model but aren’t.

Return type

list

property model

The structure’s first model (and only model if it has only one).

Return type

Model

property models

The structure’s models.

Return type

list

property resolution

The structure’s resolution.

Return type

float

property rfree

The structure’s R-free value.

Return type

float

property rvalue

The structure’s R-value.

Return type

float

property source_organism

The structure’s original organism.

Return type

float

property technique

The structure’s experimental technique.

Return type

str

property title

The structure’s text description.

Return type

str

atomium.data.atom_dict_to_atom(d, atom_id)[source]

Creates an Atom from an atom dictionary.

Parameters
  • d (dict) – the atom dictionary.

  • id (int) – the atom’s ID.

Return type

Atom

atomium.data.create_chains(model_dict)[source]

Creates a list of Chain objects from a model dictionary.

Parameters

model_dict (dict) – the model dictionary.

Return type

list

atomium.data.create_het(d, id, ligand=False, chain=None, water=False)[source]

Creates a Residue or Ligand from some atom-containing dictionary.

If there is multiple occupancy, only one position will be used.

Parameters
  • d (dict) – the dictionary to parse.

  • id (str) – the ID of the structure to make.

  • ligand (bool) – if True a ligand will be made, not a residue.

  • chain (Chain) – the Chain to assign if a ligand.

  • water (bool) – if True, the ligand will be a water ligand.

Return type

Residue or Ligand

atomium.data.create_ligands(model_dict, chains, water=False)[source]

Creates a list of Ligand objects from a model dictionary.

Parameters
  • model_dict (dict) – the model dictionary.

  • chains (list) – a list of Chain objects to assign by ID.

  • water (bool) – if True`, water ligands will be made.

Return type

list

atomium.data.data_dict_to_file(data_dict, filetype)[source]

Turns an atomium data dictionary into a File.

Parameters
  • data_dict (dict) – the data dictionary to parse.

  • filetype (str) – the file type that is being converted.

Return type

File

atomium.data.model_dict_to_model(model_dict)[source]

Takes a model dictionary and turns it into a fully processed Model object.

Parameters

model_dict (dict) – the model dictionary.

Return type

Model