add repository class

git-svn-id: https://dng.biozentrum.unibas.ch/svn/openstructure/trunk@1955 5a81b35b-ba03-0410-adc8-b2c5c5119f08

modules/io/pymod/CMakeLists.txt

@@ -10,6 +10,7 @@ endif()
 set(OST_IO_PYMOD_MODULES
   __init__.py
   hhsearch.py
+  repository.py
 )
 
 

modules/io/pymod/repository.py

+import os.path
+import string
+import os
+
+from ost import io
+
+class ModelRepository:
+  """
+  Model repository. A model repository abstracts the way that PDB files are 
+  loaded. Instead of explicitly specifying the PDB filename, only the PDB 
+  id (and optionally a chain) needs to be specified. The actual files are then 
+  resolved by the repository.
+  
+  Usage
+  -----
+  The usage pattern of the model repository is simple. After construction, 
+  models may be loaded by passing in a model id and optionally a number of 
+  chain names (see documentation for io.LoadPDB).
+  
+  Example:
+  import string
+  repos=repository.ModelRepository('path_to_pdbs', 
+                                   file_pattern='pdb%(id)s.ent.gz', 
+                                   transform=string.lower)
+  # load 1ake (note that the name is transformed by string.lower)
+  m=repos.Load('1AKE')
+  """
+  def __init__(self, directory=None, 
+               file_pattern='%(id)s.pdb',transform=str):
+    """
+    Construct new model repository
+    """
+    if directory==None:
+      self.directory_=os.getenv('PDB_PATH', '')
+    else:
+      self.directory_=directory;
+    self.file_pattern_=file_pattern
+    self.transform_=transform or string.__init__
+  def FilenameForModel(self, pdb_id, chain):
+    pdb_id=self.transform_(pdb_id)
+    basename=self.file_pattern_ % {'id' : pdb_id, 'chain' :chain, 'dir' : pdb_id[1:3]}
+    return os.path.join(self.directory_, basename)
+    
+  def Load(self, pdb_id, chains=""):
+    return io.LoadPDB(self.FilenameForModel(pdb_id, chains),
+                          chains)
+                      
+  def LoadMulti(self, pdb_id, chains=""):
+    return io.LoadMultiPDB(self.FilenameForModel(pdb_id, chains))
+