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