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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)
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PDB_REF =
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alternative_download_url =
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Retrieves all PDB entries not present in the local PDB copy. Writes a list file containing all PDB codes (optional, if listfile is given). |
Retrieves 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). |
Retrieves a big file containing all the PDB entries and some annotation to them. Returns a list of PDB codes in the index file. |
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 ... |
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 |
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. |
Retrieves a PDB structure file from the PDB server and stores it in a local file tree. The PDB structure is returned as a single string. If obsolete is 1, the file will be by default saved in a special file tree. The compression should be '.Z' or '.gz'. 'uncompress' is the command called to uncompress the files.
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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. |
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PDB_REF
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