r24407 - in /trunk/lib/structure: __init__.py files.py -- July 02, 2014 - 14:42

Author: bugman
Date: Wed Jul  2 14:42:51 2014
New Revision: 24407

URL: http://svn.gna.org/viewcvs/relax?rev=24407&view=rev
Log:
Created the new lib.structure.files module.

This currently contains the single find_pdb_files() function which will be 
used to find all *.pdb,
*.pdb.gz and *.pdb.bz2 versions of the PDB file in a given path.


Added:
    trunk/lib/structure/files.py
Modified:
    trunk/lib/structure/__init__.py

Modified: trunk/lib/structure/__init__.py
URL: 
http://svn.gna.org/viewcvs/relax/trunk/lib/structure/__init__.py?rev=24407&r1=24406&r2=24407&view=diff
==============================================================================
--- trunk/lib/structure/__init__.py     (original)
+++ trunk/lib/structure/__init__.py     Wed Jul  2 14:42:51 2014
@@ -26,6 +26,7 @@
     'angles',
     'cones',
     'conversion',
+    'files',
     'geometric',
     'mass',
     'pdb_read',

Added: trunk/lib/structure/files.py
URL: 
http://svn.gna.org/viewcvs/relax/trunk/lib/structure/files.py?rev=24407&view=auto
==============================================================================
--- trunk/lib/structure/files.py        (added)
+++ trunk/lib/structure/files.py        Wed Jul  2 14:42:51 2014
@@ -0,0 +1,61 @@
+###############################################################################
+#                                                                            
 #
+# Copyright (C) 2014 Edward d'Auvergne                                       
 #
+#                                                                            
 #
+# This file is part of the program relax (http://www.nmr-relax.com).         
 #
+#                                                                            
 #
+# This program is free software: you can redistribute it and/or modify       
 #
+# it under the terms of the GNU General Public License as published by       
 #
+# the Free Software Foundation, either version 3 of the License, or          
 #
+# (at your option) any later version.                                        
 #
+#                                                                            
 #
+# This program is distributed in the hope that it will be useful,            
 #
+# but WITHOUT ANY WARRANTY; without even the implied warranty of             
 #
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the              
 #
+# GNU General Public License for more details.                               
 #
+#                                                                            
 #
+# You should have received a copy of the GNU General Public License          
 #
+# along with this program.  If not, see <http://www.gnu.org/licenses/>.      
 #
+#                                                                            
 #
+###############################################################################
+
+# Module docstring.
+"""Module for handling different structural file formats."""
+
+# Python module imports.
+from os import F_OK, access, sep
+from re import search
+
+
+def find_pdb_files(path=None, file_root=None):
+    """Find all PDB files in the given path corresponding to the file root.
+
+    This will find all *.pdb, *.pdb.gz, and *.pdb.bz2 files, package them 
into a list, and return the list.
+
+
+    @keyword path:      The file system path to search for the files in.
+    @type path:         str
+    @keyword file_root: The file root of the files to find.  For example if 
the file is 'test.pdb.gz', then the file root is 'test'.
+    @type file_root:    str
+    """
+
+    # Initialise.
+    files = []
+
+    # The uncompressed version.
+    file = path+sep+file_root+'.pdb'
+    if access(file, F_OK):
+        files.append(file)
+
+    # The gzipped version.
+    file = path+sep+file_root+'.pdb.gz'
+    if access(file, F_OK):
+        files.append(file)
+
+    # The bzipped version.
+    file = path+sep+file_root+'.pdb.bz2'
+    if access(file, F_OK):
+        files.append(file)
+
+    # Return the file list.
+    return files