Overview

Currently available plugins and description

Current selection of plugins is determined mainly by the scientific interest of our lab. If you would like to include a new data source do not hesitate to contact us or follow a dedicated guideline.

Plugin	Description
SIFTS	Provides easy access to the SIFTS data. Adds new dataframes lpdb.pfam, lpdb.scop, lpdb.ec, lpdb.cath and an additional column in the lpdb.chains dataframes containing taxonomy information.
Biounit	Precalculates the biological assemblies from the raw PDB entries with the MakeMultimer script.
ECOD	Provides access to the ECOD data. Adds new dataframe lpdb.ecod.
DSSP	Precalculates the DSSP output for each entry in the PDB. Adds a dssp in the lpdb.entries.
PDBClustering	Enables the access to the precomputed clustering results from the RCSB. Adds the localpdb.PDB.load_clustering_data function and subsequently the clust-* column(s) in the lpdb.chains DataFrame.
PDBSeqresMapper	Provides the mapping between the names of residues in the PDB/mmCIF file and SEQRES (natural) protein sequence. Mapping is available through the localpdb.PDB.get_pdbseqres_mapping() function. Change in Nov 2023: We discontinued releases of this plugin through lbs.cent.uw.edu.pl mirror. In order to set it up, please use the localpdb_pdbseqresmapper script, e.g.: localpdb_pdbseqresmapper -db_path /home/db/localpdb -version XXXXXX (should take around 60 minutes on 20 core machine).
Socket	Calculates the coiled-coil domain annotations in the available protein structures with the Socket program. Adds a localpdb.PDB.get_socket_dict function that returns the parsed annotation for the current lpdb.entries selection.
PDBChain	Provides easy access to the precalculated PDB files corresponding to the individual chains (polymer instances)