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localpdb.PDB

localpdb.PDB()

Arguments

Argument                  Description
db_path location of the localpdb database
version version of the localpdb database to load (default: version='latest')
auto_filter automatically propagates selections performed on any of the DataFrames to other DataFrames (default: auto_filter=True). See the example below for more information.
plugins Names of the plugins to load

Example

from localpdb import PDB
lpdb = PDB(db_path='/ssd/db/localpdb', version='latest', auto_filter=True)
lpdb.entries = lpdb.entries.query(lpdb.entries.query('method == "diffraction"'))
lpdb.entries was updated and since auto_filter=True the selection will be also propagated to lpdb.chains. In other words lpdb.chains will contain only the chains corresponding to the entries present in lpdb.entries.

Attributes

Attribute Description
entries pandas.DataFrame containing all entries available in the loaded PDB release. More info.
chains pandas.DataFrame containing all chains (polymer entity instances) in the loaded PDB release. More info.
version timestamp of the loaded PDB data, in the format YYYYMMDD (e.g. 20210507)

Methods

Method                                                               Description
reset() Resets all selections performed on any of the DataFrames and restores the initial state of PDB object.
load_plugin(plugin='Name') Loads plugins and its data.
select_updates(mode='am+') Selects only the entries that were either added (mode='a') or (mode='m') or both (mode='am') in the latest PDB weekly release. In mode='am+' updates with respect to the previous localpdb version will be loaded.
extract(out_fn='backup.gz') Extracts the localpdb config (for the currently loaded version). This enables recreation of the underlying data on other machines.
search() Info available on separate page
search_seq() Info available on separate page
search_seq_motif() Info available on separate page
search_struct() Info available on separate page