Source code for proteinshake.datasets.protein_family
import json
from proteinshake.datasets import RCSBDataset
class ProteinFamilyDataset(RCSBDataset):
""" Proteins with annotated protein families (Pfam).
Each protein in the dataset has a `Pfam` attribute which stores the list of protein families.
.. admonition:: Please cite
Berman, H M et al. “The Protein Data Bank.” Nucleic acids research vol. 28,1 (2000): 235-42. doi:10.1093/nar/28.1.235
.. admonition:: Source
Raw data was obtained and modified from `RCSB Protein Data Bank <https://www.rcsb.org/>`_, originally licensed under `CC0 1.0 <https://creativecommons.org/publicdomain/zero/1.0/>`_.
.. list-table:: Dataset stats
:widths: 100
:header-rows: 1
* - # proteins
* - 31109
.. list-table:: Annotations
:widths: 25 35 45
:header-rows: 1
* - Attribute
- Key
- Sample value
* - Pfam accession code
- :code:`protein['protein']['Pfam']`
- `['PF00102']`
"""
description = 'Protein Families'
def __init__(self, pfam_version='34.0', query=[['rcsb_polymer_entity_annotation.type','exact_match','Pfam']], **kwargs):
self.pfam_version = pfam_version
super().__init__(query=query, **kwargs)
def add_protein_attributes(self, protein):
with open(f'{self.root}/raw/files/{protein["protein"]["ID"]}.annot.json','r') as file:
annot = json.load(file)
pfams = []
for a in annot['rcsb_polymer_entity_annotation']:
if a['type'] == 'Pfam':
# pfams.append(a['name'])
pfams.append(a['annotation_id'])
protein['protein']['Pfam'] = pfams
return protein