PDB Sequence Clusters

This module defines functions for handling PDB sequence clusters.

prody.proteins.pdbclusters.fetchPDBClusters(sqid=None)

Retrieve PDB sequence clusters. PDB sequence clusters are results of the regular clustering of polymer entities in the PDB. They are available at: https://cdn.rcsb.org/resources/sequence/clusters/ as clusters-by-entity-sqid.txt (the legacy bc-sqid.out files have been deprecated by RCSB).

This function will download the cluster data and save it after compressing in your home directory in .prody/pdbclusters. Cluster data can be loaded using loadPDBClusters() function and be accessed using listPDBCluster().

prody.proteins.pdbclusters.listPDBCluster(pdb, entity=1, sqid=95)

Returns the PDB sequence cluster that contains polymer entity in structure pdb for sequence identity level sqid. The cluster is returned as a list of tuples, e.g. [('1XXX', '1'), ]. Note that RCSB now clusters by polymer entity (not by individual chain), so entity is an entity identifier such as 1 and the same PDB identifier may appear more than once across clusters if the structure has multiple entities.

Before this function is used, fetchPDBClusters() needs to be called. This function will load the PDB sequence clusters for sqid automatically using loadPDBClusters().

prody.proteins.pdbclusters.loadPDBClusters(sqid=None)

Load previously fetched PDB sequence clusters from disk to memory.