Bio.PDB.PDBList module¶
Access the PDB over the internet (e.g. to download structures).
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class
Bio.PDB.PDBList.
PDBList
(server='ftp://ftp.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)
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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 '¶
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__init__
(self, server='ftp://ftp.wwpdb.org', pdb=None, obsolete_pdb=None, verbose=True)¶ 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.
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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.
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get_recent_changes
(self)¶ 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
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get_all_entries
(self)¶ Retrieve the big file containing all the PDB entries and some annotation.
Returns a list of PDB codes in the index file.
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get_all_obsolete
(self)¶ 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 ...
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retrieve_pdb_file
(self, 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
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update_pdb
(self, file_format=None)¶ 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.
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download_pdb_files
(self, 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 availbe as mmtf. (default: False)
pdir (string) – put the file in this directory (default: create a PDB-style directory tree)
- Returns
filenames
- Return type
string
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download_entire_pdb
(self, listfile=None, file_format=None)¶ Retrieve all PDB entries not present in the local PDB copy.
- Parameters
listfile – filename to which all PDB codes will be written (optional)
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}
NOTE. The default download format has changed from PDB to PDBx/mmCif
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download_obsolete_entries
(self, listfile=None, file_format=None)¶ Retrieve all obsolete PDB entries not present in local obsolete PDB copy.
- Parameters
listfile – filename to which all PDB codes will be written (optional)
file_format – file format. Available options: “mmCif” (default, PDBx/mmCif file), “pdb” (format PDB), “xml” (PMDML/XML format),
NOTE. The default download format has changed from PDB to PDBx/mmCif
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get_seqres_file
(self, savefile='pdb_seqres.txt')¶ Retrieve and save a (big) file containing all the sequences of PDB entries.
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