pwem.convert.pdb_list module

Access the PDB over the internet (e.g. to download structures).

class pwem.convert.pdb_list.PDBList(server='https://files.wwpdb.org', pdb=None, obsolete_pdb=None, verbose=True)

Bases: object

Quick access to the structure lists on the PDB or its mirrors.

This class provides quick access to the structure lists on the PDB server or its mirrors. The structure lists contain four-letter PDB codes, indicating that structures are new, have been modified or are obsolete. The lists are released on a weekly basis.

It also provides a function to retrieve PDB files from the server. To use it properly, prepare a directory /pdb or the like, where PDB files are stored.

All available file formats (PDB, PDBx/mmCif, PDBML, mmtf) are supported. Please note that large structures (containing >62 chains and/or 99999 ATOM lines) are no longer stored as a single PDB file and by default (when PDB format selected) are not downloaded.

Large structures can be downloaded in other formats, including PDBx/mmCif or as a .tar file (a collection of PDB-like formatted files for a given structure).

If you want to use this module from inside a proxy, add the proxy variable to your environment, e.g. in Unix: export HTTP_PROXY=’http://realproxy.charite.de:888’ (This can also be added to ~/.bashrc)

Initialize the class with the default server or a custom one.

Argument pdb is the local path to use, defaulting to the current directory at the moment of initialisation.

PDB_REF = '\n    The Protein Data Bank: a computer-based archival file for macromolecular structures.\n    F.C.Bernstein, T.F.Koetzle, G.J.B.Williams, E.F.Meyer Jr, M.D.Brice, J.R.Rodgers, O.Kennard, T.Shimanouchi, M.Tasumi\n    J. Mol. Biol. 112 pp. 535-542 (1977)\n    http://www.pdb.org/.\n    '

download_pdb_files(pdb_codes, obsolete=False, pdir=None, file_format=None, overwrite=False)

Fetch set of PDB structure files from the PDB server and stores them locally.

The PDB structure’s file name is returned as a single string. If obsolete == True, the files will be saved in a special file tree.

Parameters

• pdb_codes (list of strings) – a list of 4-symbols structure Ids from PDB

• file_format –

  File format. Available options:

  • ”mmCif” (default, PDBx/mmCif file),

  • ”pdb” (format PDB),

  • ”xml” (PMDML/XML format),

  • ”mmtf” (highly compressed),

  • ”bundle” (PDB formatted archive for large structure)

• overwrite (bool) – if set to True, existing structure files will be overwritten. Default: False

• obsolete (bool) – Has a meaning only for obsolete structures. If True, download the obsolete structure to ‘obsolete’ folder, otherwise download won’t be performed. This option doesn’t work for mmtf format as obsoleted structures are not available as mmtf. (default: False)

• pdir (string) – put the file in this directory (default: create a PDB-style directory tree)

Returns

filenames

Return type

string

get_all_entries()

Retrieve the big file containing all the PDB entries and some annotation.

Returns a list of PDB codes in the index file.

get_all_obsolete()

Return a list of all obsolete entries ever in the PDB.

Returns a list of all obsolete pdb codes that have ever been in the PDB.

Gets and parses the file from the PDB server in the format (the first pdb_code column is the one used). The file looks like this:

 LIST OF OBSOLETE COORDINATE ENTRIES AND SUCCESSORS
OBSLTE    31-JUL-94 116L     216L
...
OBSLTE    29-JAN-96 1HFT     2HFT
OBSLTE    21-SEP-06 1HFV     2J5X
OBSLTE    21-NOV-03 1HG6
OBSLTE    18-JUL-84 1HHB     2HHB 3HHB
OBSLTE    08-NOV-96 1HID     2HID
OBSLTE    01-APR-97 1HIU     2HIU
OBSLTE    14-JAN-04 1HKE     1UUZ
...

get_recent_changes()

Return three lists of the newest weekly files (added,mod,obsolete).

Reads the directories with changed entries from the PDB server and returns a tuple of three URL’s to the files of new, modified and obsolete entries from the most recent list. The directory with the largest numerical name is used. Returns None if something goes wrong.

Contents of the data/status dir (20031013 would be used);:

drwxrwxr-x 2 1002 sysadmin 512 Oct 6 18:28 20031006 drwxrwxr-x 2 1002 sysadmin 512 Oct 14 02:14 20031013 -rw-r–r– 1 1002 sysadmin 1327 Mar 12 2001 README

static get_status_list(url)

Retrieve a list of pdb codes in the weekly pdb status file from given URL.

Used by get_recent_changes. Typical contents of the list files parsed by this method is now very simply - one PDB name per line.

retrieve_pdb_file(pdb_code, obsolete=False, pdir=None, file_format=None, overwrite=False)

Fetch PDB structure file from PDB server, and store it locally.

The PDB structure’s file name is returned as a single string. If obsolete == True, the file will be saved in a special file tree.

NOTE. The default download format has changed from PDB to PDBx/mmCif

Parameters

• pdb_code (string) – 4-symbols structure Id from PDB (e.g. 3J92).

• file_format (string) –

  File format. Available options:

  • ”mmCif” (default, PDBx/mmCif file),

  • ”pdb” (format PDB),

  • ”xml” (PDBML/XML format),

  • ”mmtf” (highly compressed),

  • ”bundle” (PDB formatted archive for large structure)

• overwrite (bool) – if set to True, existing structure files will be overwritten. Default: False

• obsolete (bool) – Has a meaning only for obsolete structures. If True, download the obsolete structure to ‘obsolete’ folder, otherwise download won’t be performed. This option doesn’t work for mmtf format as obsoleted structures aren’t stored in mmtf. Also doesn’t have meaning when parameter pdir is specified. Note: make sure that you are about to download the really obsolete structure. Trying to download non-obsolete structure into obsolete folder will not work and you face the “structure doesn’t exists” error. Default: False

• pdir (string) – put the file in this directory (default: create a PDB-style directory tree)

Returns

filename

Return type

string

update_pdb(file_format=None, with_assemblies=False)

Update your local copy of the PDB files.

I guess this is the ‘most wanted’ function from this module. It gets the weekly lists of new and modified pdb entries and automatically downloads the according PDB files. You can call this module as a weekly cron job.