pdbsearch.rcsb
- pdbsearch.rcsb.apply_pagination(query, start, limit)[source]
Creates a query’s
request_optionsand applies pagination information to it, or an instruction to get all data.- Parameters
query (dict) – the RCSB query object.
start (int) – the start location.
limit (int) – the number of results to return (or
Noneto get everything)
- pdbsearch.rcsb.apply_query(query, kwargs)[source]
Adds the query component to the overall query object. It uses whatever leftover keyword arguments are passed to the search function and uses these in a chain of AND queries.
- Parameters
query (dict) – the RCSB query object.
kwargs (dict) – the keyword arguments passed to the search function.
- pdbsearch.rcsb.apply_sort(query, sort)[source]
Applies sort terms to a query’s
request_options.- Parameters
query (dict) – the RCSB query object.
sort – the sort term(s).
- pdbsearch.rcsb.get_query_attribute(kwarg)[source]
Takes a proposed query property and modifies it as needed based on suffixes or shorthand.
- Parameters
kwarg (str) – the keyword argument passed to the search function.
- Return type
str
- pdbsearch.rcsb.get_query_operator(kwarg, value)[source]
Takes a key-value pair passed to the search function and works out what operator should be used (equals, less than, within etc.).
- Parameters
kwarg (str) – the keyword argument passed to the search function.
value – the search value.
- Return type
str
- pdbsearch.rcsb.get_query_parameters(property, value)[source]
Takes a key-value pair passed to the search function and turns it into a parameters dictionary representing that search criterion.
- Parameters
property (str) – the keyword name.
value – the search value.
- Return type
dict
- pdbsearch.rcsb.search(start=0, limit=10, sort=None, **kwargs)[source]
Searches for PDB codes. You can choose how many to get and from what starting point.
Sort terms can either be formal RCSB attributes, or a shorthand such as ‘resolution’ or ‘code’. If you supply a list of terms, these will be applied in turn.
- Parameters
start (int) – the start index (default 0).
limit (int) – how many codes to return (default 10).
sort – the sort term, or list of sort terms.
- Return type
list
- pdbsearch.rcsb.send_request(query)[source]
Sends a query dictionary to the RCSB search API. If a valid response is received, this will be returned in JSON format. Otherwise
Nonewill be returned.- Parameters
query (dict) – the query, formatted to RCSB specifications.
- Return type
dict
- pdbsearch.rcsb.sort_term_to_sort_dict(term)[source]
Converts a single string to a RCSB sort modifier. If a ‘-’ is on the front of the string, the search will be made ascending - otherwise it is descending.
The string should be one of the terms given at https://search.rcsb.org/search-attributes.html, or one of a few shorthands (see code).
- Parameters
term (str) – the sort term.
- Return type
dict