r14901 - in /1.3: generic_fns/structure/main.py prompt/structure.py -- October 24, 2011 - 15:34

Author: bugman
Date: Mon Oct 24 15:34:04 2011
New Revision: 14901

URL: http://svn.gna.org/viewcvs/relax?rev=14901&view=rev
Log:
The structure.read_pdb user function can now handle bzip2 or gzip compressed 
PDB files.


Modified:
    1.3/generic_fns/structure/main.py
    1.3/prompt/structure.py

Modified: 1.3/generic_fns/structure/main.py
URL: 
http://svn.gna.org/viewcvs/relax/1.3/generic_fns/structure/main.py?rev=14901&r1=14900&r2=14901&view=diff
==============================================================================
--- 1.3/generic_fns/structure/main.py (original)
+++ 1.3/generic_fns/structure/main.py Mon Oct 24 15:34:04 2011
@@ -295,10 +295,14 @@
     # The file path.
     file_path = get_file_path(file, dir)
 
-    # Try adding '.pdb' to the end of the file path, if the file can't be 
found.
+    # Try adding file extensions to the end of the file path, if the file 
can't be found.
+    file_path_orig = file_path
     if not access(file_path, F_OK):
-        file_path_orig = file_path
-        file_path = file_path + '.pdb'
+        # List of possible extensions.
+        for ext in ['.pdb', '.gz', '.pdb.gz', '.bz2', '.pdb.bz2']:
+            # Add the extension if the file can be found.
+            if access(file_path+ext, F_OK):
+                file_path = file_path + ext
 
     # Test if the file exists.
     if not access(file_path, F_OK):

Modified: 1.3/prompt/structure.py
URL: 
http://svn.gna.org/viewcvs/relax/1.3/prompt/structure.py?rev=14901&r1=14900&r2=14901&view=diff
==============================================================================
--- 1.3/prompt/structure.py (original)
+++ 1.3/prompt/structure.py Mon Oct 24 15:34:04 2011
@@ -300,6 +300,8 @@
         Setting the molecule name allows the molecule within the PDB (within 
one model) to have a custom name.  If not set, then the molecules will be 
named after the file name, with the molecule number appended if more than one 
exists.
 
         Note that relax will complain if it cannot work out what to do.
+
+        This is able to handle uncompressed, bzip2 compressed files, or gzip 
compressed files automatically.  The full file name including extension can 
be supplied, however, if the file cannot be found, this function will search 
for the file name with '.bz2' appended followed by the file name with '.gz' 
appended.
         """
     read_pdb._doc_examples = """
         To load all structures from the PDB file 'test.pdb' in the directory 
'~/pdb', including all