mmtfPyspark.webfilters.customReportQuery module

customReportQuery.py

This filter runs an SQL query on specified PDB metadata and annotation fields retrived using RCSB PDB RESTful web services. The fields are then queried and the resulting PDB IDs are used to filter the data. The input to the filter consists of an SQL WHERE clause, and list data columns availible from RCSB PDB web services.

References

Examples

Find PDB entries with Enzyme classification number 2.7.11.1 and source organism Homo sapiens:

>>> pdb = read_full_sequence_files(sc)
>>> whereClause = "WHERE ecNo='2.7.11.1' AND source='Homo sapiens'"
>>> pdb = pdb.filter(RcsbWebserviceFilter(whereClause, "ecNo","source"))
class CustomReportQuery(whereClause, fields)[source]

Bases: object

Filters using an SQL query on the specified fields

Attributes

whereClause (str) WHERE Clause of SQL statement
fields (str, list) one or more field names to be used in query

Methods

__call__(t) Call self as a function.