count
#
- biotite.database.rcsb.count(query, return_type='entry', group_by=None, content_types=('experimental',))[source]#
Count PDB entries that meet the given query requirements, via the RCSB search API.
This function requires an internet connection.
- Parameters:
- queryQuery
The search query.
- return_type{‘entry’, ‘assembly’, ‘polymer_entity’, ‘non_polymer_entity’, ‘polymer_instance’}, optional
The type of the counted identifiers:
'entry'
: All macthing PDB entries are counted.'assembly'
: All matching assemblies are counted.'polymer_entity'
: All matching polymeric entities are counted.'non_polymer_entity'
: All matching non-polymeric entities are counted.'polymer_instance'
: All matching chains are counted.
- group_byGrouping
If this parameter is set, the number of groups is returned instead.
- content_typesiterable of {“experimental”, “computational”}, optional
Specify whether experimental and computational structures should be included. At least one of them needs to be specified. By default only experimental structures are included. Note, that identifiers for computational structures cannot be downloaded via
biotite.database.rcsb.fetch()
as they point to AlphaFold DB and ModelArchive.
- Returns:
- countint
The total number of PDB IDs (or groups) that would be returned by calling
search()
using the same parameters.
Notes
If group_by is set, the number of results may be lower than in an ungrouped query, as grouping is not applicable to all structures. For example a DNA structure has no associated Uniprot accession and hence is omitted by
UniprotGrouping
.Examples
>>> query = FieldQuery("reflns.d_resolution_high", less_or_equal=0.6) >>> print(count(query)) 9 >>> ids = search(query) >>> print(sorted(ids)) ['1EJG', '1I0T', '3NIR', '3P4J', '4JLJ', '5D8V', '5NW3', '7ATG', '7R0H']