Dali Server Functions

This module defines functions for Dali searching Protein Data Bank.

class prody.database.dali.DaliRecord(url, pdbId, chain, subset='fullPDB', localFile=False, **kwargs)[source]

A class to store results from Dali PDB search.

fetch(url=None, localFile=False, **kwargs)[source]

Get Dali record from url or file.

Parameters:

  • url (str) – url of Dali results page or local dali results file If None then the url already associated with the DaliRecord object is used.

  • localFile (bool) – whether provided url is a path for a local dali results file

  • timeout (int) – amount of time until the query times out in seconds default value is 120

  • localfolder (str) – folder in which to find the local file default is the current folder

filter(cutoff_len=None, cutoff_rmsd=None, cutoff_Z=None, cutoff_identity=None, stringency=False)[source]

Filters a PDBList by a given set of cutoffs and returns a list of PDB IDs where PDBs that matched have been removed. PDBs that satisfy _any_ of the following criteria will be filtered out. (1) Length of aligned residues < cutoff_len (must be an integer or a float between 0 and 1); (2) RMSD < cutoff_rmsd (must be a positive number); (3) Z score < cutoff_Z (must be a positive number); (4) Identity > cutoff_identity (must be an integer or a float between 0 and 1).

Setting the stringency flag to True changes the behavior so that all filtering is by stringency. In this case, PDBs that satisfy _any_ of the following criteria will be filtered out:

  1. Length of aligned residues < cutoff_len (must be an integer or a float between 0 and 1); (unchanged)

  2. RMSD > cutoff_rmsd (must be a positive number); (inverted)

  3. Z score < cutoff_Z (must be a positive number); (unchanged)

  4. Identity < cutoff_identity (must be an integer or a float between 0 and 1). (inverted)

Leaving stringency False maintains old behavior.

getFilterList()[source]

Returns a list of PDB IDs and chains for the entries that were filtered out

getHits()[source]

Returns the dictionary associated with the DaliRecord

getMapping(key)[source]

Get mapping for a particular entry in the DaliRecord

getMappings()[source]

Get all mappings in the DaliRecord

getPDBs(filtered=True)[source]

Returns PDB list (filters may be applied)

getTitle()[source]

Return the title of the record

property mappings

Get all mappings in the DaliRecord

prody.database.dali.daliFilterMultimer(atoms, dali_rec, n_chains=None, reverse=False)[source]

Filters multimers to only include chains with Dali mappings.

Parameters:

  • atoms (Atomic) – the multimer to be filtered

  • dali_rec (DaliRecord) – the DaliRecord object with which to filter chains

  • n_chains – the number of chains in multimers to keep Default is None, keeping all multimers

  • n_chains – int

  • reverse (bool) – whether to reverse filtering to exclude by n_chain Default is False

prody.database.dali.daliFilterMultimers(structures, dali_rec, n_chains=None, reverse=False)[source]

A wrapper for daliFilterMultimer to apply to multiple structures.

Parameters:

  • structures (list) – a list of Atomic objects to be filtered

  • dali_rec (DaliRecord) – the DaliRecord object with which to filter chains

  • n_chains – the number of chains in multimers to keep Default is None, keeping all multimers

  • n_chains – int

  • reverse (bool) – whether to reverse filtering to exclude by n_chain Default is False

prody.database.dali.searchDali(pdb, chain=None, subset='fullPDB', daliURL=None, **kwargs)[source]

Search Dali server with input of PDB ID (or local PDB file) and chain ID. Dali server: http://ekhidna2.biocenter.helsinki.fi/dali/

Parameters:

  • pdb – PDB code or local PDB file for the protein to be searched

  • chain (str) – chain identifier (only one chain can be assigned for PDB)

  • subset (str) – fullPDB, PDB25, PDB50, PDB90