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Remove deprecated parameters

Obsolete parameters (which were rarely specified by users anyway) gave
warnings in version 1.57. They should be able to be safely removed now.
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1 parent b825091 commit f9aba618d164e75abf42efa5585eb8a8f1575a11 @DavidCain DavidCain committed with etal Jan 9, 2013
Showing with 4 additions and 20 deletions.
  1. +4 −20 Bio/PDB/PDBList.py
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@@ -28,9 +28,6 @@
import shutil
import urllib
from urllib2 import urlopen as _urlopen # urllib made too many FTP conn's
-import warnings
-
-from Bio import BiopythonDeprecationWarning
class PDBList(object):
@@ -171,32 +168,19 @@ def get_all_obsolete(self):
obsolete.append(pdb)
return obsolete
- def retrieve_pdb_file(self, pdb_code, obsolete=0, compression=None,
- uncompress=None, pdir=None):
+ def 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.
- The PDB structure is returned as a single string.
- If obsolete==1, the file will be saved in a special file tree.
- If uncompress is specified, a system utility will decompress the .gz
- archive. Otherwise, Python gzip utility will handle it.
- compression does nothing, as all archives are already in .gz format
+
+ 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
"""
- # Alert the user about deprecated parameters
- if compression is not None:
- warnings.warn("PDB file servers now only host .gz archives: "
- "the compression parameter will not do anything",
- BiopythonDeprecationWarning)
- if uncompress is not None:
- warnings.warn("Decompression is handled with the gzip module: "
- "the uncompression parameter will not do anything",
- BiopythonDeprecationWarning)
-
# Get the structure
code = pdb_code.lower()
archive_fn = "pdb%s.ent.gz" % code

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