PDB Blast Search¶
This module defines functions for blast searching Protein Data Bank.
A class to store results from ProteinDataBank blast search.
Instantiate a PDBlast object instance.
Returns a dictionary containing structure and alignment information for the hit with highest sequence identity.
getHits(percent_identity=90.0, percent_overlap=70.0, chain=False)¶
Returns a dictionary in which PDB identifiers are mapped to structure and alignment information.
- percent_identity (float) – PDB hits with percent sequence identity equal
to or higher than this value will be returned, default is
- percent_overlap (float) – PDB hits with percent coverage of the query
sequence equivalent or better will be returned, default is
- chain (bool) – if chain is True, individual chains in a PDB file will be considered as separate hits , default is False
- percent_identity (float) – PDB hits with percent sequence identity equal to or higher than this value will be returned, default is
Returns parameters used in blast search.
Returns the query sequence that was used in the search.
blastPDB(sequence, filename=None, **kwargs)¶
PDBBlastRecordinstance that contains results from blast searching of ProteinDataBank database sequence using NCBI blastp.
hitlist_size (default is
250) and expect (default is
1e-10) search parameters can be adjusted by the user. sleep keyword argument (default is
2seconds) determines how long to wait to reconnect for results. Sleep time is doubled when results are not ready. timeout (default is 120s) determines when to give up waiting for the results.