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"""
PDBe (Protein Data Bank in Europe)
@website https://www.ebi.ac.uk/pdbe
@provide-api yes (https://www.ebi.ac.uk/pdbe/api/doc/search.html),
unlimited
@using-api yes
@results python dictionary (from json)
@stable yes
@parse url, title, content, img_src
"""
from json import loads
from flask_babel import gettext
categories = ['science']
hide_obsolete = False
# status codes of unpublished entries
pdb_unpublished_codes = ['HPUB', 'HOLD', 'PROC', 'WAIT', 'AUTH', 'AUCO', 'REPL', 'POLC', 'REFI', 'TRSF', 'WDRN']
# url for api query
pdbe_solr_url = 'https://www.ebi.ac.uk/pdbe/search/pdb/select?'
# base url for results
pdbe_entry_url = 'https://www.ebi.ac.uk/pdbe/entry/pdb/{pdb_id}'
# link to preview image of structure
pdbe_preview_url = 'https://www.ebi.ac.uk/pdbe/static/entry/{pdb_id}_deposited_chain_front_image-200x200.png'
def request(query, params):
params['url'] = pdbe_solr_url
params['method'] = 'POST'
params['data'] = {
'q': query,
'wt': "json" # request response in parsable format
}
return params
def construct_body(result):
# set title
title = result['title']
# construct content body
content = """{title}<br />{authors} {journal} <strong>{volume}</strong> {page} ({year})"""
# replace placeholders with actual content
try:
if result['journal']:
content = content.format(
title=result['citation_title'],
authors=result['entry_author_list'][0], journal=result['journal'], volume=result['journal_volume'],
page=result['journal_page'], year=result['citation_year'])
else:
content = content.format(
title=result['citation_title'],
authors=result['entry_author_list'][0], journal='', volume='', page='', year=result['release_year'])
img_src = pdbe_preview_url.format(pdb_id=result['pdb_id'])
except (KeyError):
content = None
img_src = None
# construct url for preview image
try:
img_src = pdbe_preview_url.format(pdb_id=result['pdb_id'])
except (KeyError):
img_src = None
return [title, content, img_src]
def response(resp):
results = []
json = loads(resp.text)['response']['docs']
# parse results
for result in json:
# catch obsolete entries and mark them accordingly
if result['status'] in pdb_unpublished_codes:
continue
if hide_obsolete:
continue
if result['status'] == 'OBS':
# expand title to add some sort of warning message
title = gettext('{title} (OBSOLETE)').format(title=result['title'])
superseded_url = pdbe_entry_url.format(pdb_id=result['superseded_by'])
# since we can't construct a proper body from the response, we'll make up our own
msg_superseded = gettext("This entry has been superseded by")
content = '<em>{msg_superseded} \<a href="{url}">{pdb_id}</a></em>'.format(
msg_superseded=msg_superseded,
url=superseded_url,
pdb_id=result['superseded_by'], )
# obsoleted entries don't have preview images
img_src = None
else:
title, content, img_src = construct_body(result)
results.append({
'url': pdbe_entry_url.format(pdb_id=result['pdb_id']),
'title': title,
'content': content,
'img_src': img_src
})
return results
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