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# status codes of unpublished entries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