r5353 - /1.3/generic_fns/structure/main.py -- April 07, 2008 - 14:20

Author: bugman
Date: Mon Apr  7 14:20:06 2008
New Revision: 5353

URL: http://svn.gna.org/viewcvs/relax?rev=5353&view=rev
Log:
Converted the read_pdb() function to the new relax design.


Modified:
    1.3/generic_fns/structure/main.py

Modified: 1.3/generic_fns/structure/main.py
URL: 
http://svn.gna.org/viewcvs/relax/1.3/generic_fns/structure/main.py?rev=5353&r1=5352&r2=5353&view=diff
==============================================================================
--- 1.3/generic_fns/structure/main.py (original)
+++ 1.3/generic_fns/structure/main.py Mon Apr  7 14:20:06 2008
@@ -35,8 +35,42 @@
 
 
 
-def read_pdb(run=None, file=None, dir=None, model=None, load_seq=1, fail=1, 
verbosity=1):
-    """The pdb loading function."""
+def read_pdb(file=None, dir=None, model=None, parser='scientific', 
spin_id=None, load_seq=True, fail=True, verbosity=1):
+    """The PDB loading function.
+
+    Parsers
+    =======
+
+    Currently only the Scientific Python parser is available for reading PDB 
files.  This parser is
+    selected only if the parser keyword argument is set to 'scientific'.
+
+
+    @keyword file:          The name of the PDB file to read.
+    @type file:             str
+    @keyword dir:           The directory where the PDB file is located.  If 
set to None, then the
+                            file will be searched for in the current 
directory.
+    @type dir:              str or None
+    @keyword model:         The PDB model to extract from the file.  If set 
to None, then all models
+                            will be loaded.
+    @type model:            int or None
+    @keyword parser:        The parser to be used to read the PDB file.
+    @type parser:           str
+    @keyword spid_id:       The spin identification string.
+    @type spid_id:          str
+    @keyword load_seq:      A flag which, if True, will cause the sequence 
to be loaded from the
+                            structural data object into the relax data store.
+    @type load_seq:         bool
+    @keyword fail:          A flag which, if True, will cause a RelaxError 
to be raised if the PDB
+                            file does not exist.  If False, then a 
RelaxWarning will be trown
+                            instead.
+    @type fail:             bool
+    @keyword verbosity:     The amount of information to print to screen.  
Zero corresponds to
+                            minimal output while higher values increase the 
amount of output.  The
+                            default value is 1.
+    @type verbosity:        int
+    @raise RelaxFileError:  If the fail flag is set, then a RelaxError is 
raised if the PDB file
+                            does not exist.
+    """
 
     # Tests.
     ########
@@ -48,7 +82,7 @@
     # Alias the current data pipe.
     cdp = relax_data_store[relax_data_store.current_pipe]
 
-    # Test if PDB data corresponding to the run already exists.
+    # Test if structural data already exists.
     if hasattr(cdp, 'struct'):
         raise RelaxPdbError