r5422 - /1.3/prompt/structure.py -- April 08, 2008 - 14:19

Author: bugman
Date: Tue Apr  8 14:19:27 2008
New Revision: 5422

URL: http://svn.gna.org/viewcvs/relax?rev=5422&view=rev
Log:
Updated the structure.read_pdb() user function.

The arguments load_seq and spin_id have been removed as this functionality 
has been shifted into the
new user function structure.load_spins().


Modified:
    1.3/prompt/structure.py

Modified: 1.3/prompt/structure.py
URL: 
http://svn.gna.org/viewcvs/relax/1.3/prompt/structure.py?rev=5422&r1=5421&r2=5422&view=diff
==============================================================================
--- 1.3/prompt/structure.py (original)
+++ 1.3/prompt/structure.py Tue Apr  8 14:19:27 2008
@@ -287,8 +287,8 @@
         generic_fns.structure.main.load_spins(spin_id=spin_id)
 
 
-    def read_pdb(self, file=None, dir=None, model=None, parser='scientific', 
load_seq=True, spin_id='@N'):
-        """The pdb loading function.
+    def read_pdb(self, file=None, dir=None, model=None, parser='scientific'):
+        """The PDB loading function.
 
         Keyword Arguments
         ~~~~~~~~~~~~~~~~~
@@ -300,10 +300,6 @@
         model:  The PDB model number.
 
         parser:  The PDB parser used to read the file.
-
-        load_seq:  A flag specifying whether the sequence should be loaded 
from the PDB file.
-
-        spin_id:  The spin identification string.
 
 
         Description
@@ -315,12 +311,6 @@
 
         Currently only the Scientific Python PDB parser can be used to read 
structural data.
         Therefore the 'parser' argument should be set to the string 
'scientific'.
-
-        To load the molecule, residue, and spin system sequence from the PDB 
file, set the
-        'load_seq' flag to True.  If the sequence has previously been 
loaded, then this flag will be
-        ignored.  The 'spin_id' string will be used to determine which 
molecules, which residues,
-        and which atoms will be loaded for the analysis.  If this argument 
is set to None, then all
-        molecules, all residues, and all atoms in the PDB file will be 
loaded.
 
 
         Example
@@ -345,9 +335,7 @@
             text = text + "file=" + `file`
             text = text + ", dir=" + `dir`
             text = text + ", model=" + `model`
-            text = text + ", parser=" + `parser`
-            text = text + ", load_seq=" + `load_seq`
-            text = text + ", spin_id=" + `spin_id` + ")"
+            text = text + ", parser=" + `parser + ")"`
             print text
 
         # File name.
@@ -366,16 +354,8 @@
         if type(parser) != str:
             raise RelaxStrError, ('PDB parser', parser)
 
-        # The load sequence argument.
-        if type(load_seq) != bool:
-            raise RelaxBoolError, ('load sequence flag', load_seq)
-
-        # Spin identifier.
-        if spin_id != None and type(spin_id) != str:
-            raise RelaxNoneStrError, ('spin identifier', spin_id)
-
         # Execute the functional code.
-        generic_fns.structure.main.read_pdb(file=file, dir=dir, model=model, 
parser=parser, load_seq=load_seq, spin_id=spin_id)
+        generic_fns.structure.main.read_pdb(file=file, dir=dir, model=model, 
parser=parser)
 
 
     def vectors(self, heteronuc='N', proton='H', spin_id=None, verbosity=1):