atomium.files.file

Contains the File class.

class atomium.files.file.File[source]

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

filetype

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

Return type:str
code

The unique database identifer for this structure.

Return type:str
title

The structure’s text description.

Return type:str
deposition_date

The date the structure was submitted for publication.

Return type:datetime.date
classification

The structure’s formal classification.

Return type:str
keywords

The structure’s keyword descriptors.

Return type:list
authors

The structure’s authors.

Return type:list
technique

The structure’s experimental technique.

Return type:str
source_organism

The structure’s original organism.

Return type:float
expression_system

The organism the structure was expressed in.

Return type:float
resolution

The structure’s resolution.

Return type:float
rvalue

The structure’s R-value.

Return type:float
rfree

The structure’s R-free value.

Return type:float
assemblies

The structure’s assembly instructions.

Return type:list
models

The structure’s models.

Return type:list
model

The structure’s primary Model.

Return type:Model
generate_assembly(id)[source]

Creates a Model from the current model and the instructions contained in one of the Pdb’s assemblies, which you specify.

Parameters:id (int) – The assembly to use to generate the assembly.
Raises:ValueError – if you give an ID which doesn’t correspond to a assembly.
Return type:Model
best_assembly

Returns the ‘best’ biological assembly for this Pdb - the one with the lowest (most negative) delta energy.

If there are no assemblies, None is returned.

Return type:Model
generate_best_assembly()[source]

Generates the ‘best’ biological assembly for this Pdb - the one with the lowest (most negative) delta energy.

If there are no assemblies, the original model will be returned.

Return type:Model
save(path)[source]

Saves the File to the location specified. The file extension in the path given will be used to determine what file type to save as.

Currently supported extensions are .pdb and .xyz (.cif coming soon).

Parameters:path (str) – The path to save to.