Package Bio :: Package PDB :: Module PDBList' :: Class PDBList
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Class PDBList

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object --+
         |
        PDBList

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.

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)

Instance Methods [hide private]
 
__init__(self, server='ftp://ftp.wwpdb.org', pdb='/usr/lib64/python2.6/site-packages', obsolete_pdb=None)
Initialize the class with the default server or a custom one.
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download_entire_pdb(self, listfile=None)
Retrieve all PDB entries not present in the local PDB copy.
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download_obsolete_entries(self, listfile=None)
Retrieve all obsolete PDB entries not present in the local obsolete PDB copy.
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get_all_entries(self)
Retrieves a big file containing all the PDB entries and some annotation to them.
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get_all_obsolete(self)
Returns a list of all obsolete entries ever in the PDB.
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get_recent_changes(self)
Returns three lists of the newest weekly files (added,mod,obsolete).
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get_seqres_file(self, savefile='pdb_seqres.txt')
Retrieves a (big) file containing all the sequences of PDB entries and writes it to a file.
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get_status_list(self, url)
Retrieves a list of pdb codes in the weekly pdb status file from the given URL.
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retrieve_pdb_file(self, pdb_code, obsolete=False, pdir=None)
Retrieves a PDB structure file from the PDB server and stores it in a local file tree.
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update_pdb(self)
I guess this is the 'most wanted' function from this module.
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Inherited from object: __delattr__, __format__, __getattribute__, __hash__, __new__, __reduce__, __reduce_ex__, __repr__, __setattr__, __sizeof__, __str__, __subclasshook__

Class Variables [hide private]
  PDB_REF = '\n The Protein Data Bank: a computer-based archi...
  alternative_download_url = 'http://www.rcsb.org/pdb/files/'
Properties [hide private]

Inherited from object: __class__

Method Details [hide private]

__init__(self, server='ftp://ftp.wwpdb.org', pdb='/usr/lib64/python2.6/site-packages', obsolete_pdb=None)
(Constructor)

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Initialize the class with the default server or a custom one.
Overrides: object.__init__

download_entire_pdb(self, listfile=None)

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Retrieve all PDB entries not present in the local PDB copy.

Writes a list file containing all PDB codes (optional, if listfile is given).

download_obsolete_entries(self, listfile=None)

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Retrieve all obsolete PDB entries not present in the local obsolete PDB copy.

Writes a list file containing all PDB codes (optional, if listfile is given).

get_all_entries(self)

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Retrieves a big file containing all the PDB entries and some annotation to them. Returns a list of PDB codes in the index file.

get_all_obsolete(self)

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Returns 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(self)

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Returns 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

get_status_list(self, url)

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Retrieves a list of pdb codes in the weekly pdb status file from the given URL. Used by get_recent_files.

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

retrieve_pdb_file(self, pdb_code, obsolete=False, pdir=None)

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Retrieves a PDB structure file from the PDB server and stores it in a local file tree.

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.

@param pdir: put the file in this directory (default: create a PDB-style directory tree) @type pdir: string

@return: filename @rtype: string

update_pdb(self)

source code 
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 cronjob.

Class Variable Details [hide private]

PDB_REF

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