r7350 - in /1.3/generic_fns/structure: api_base.py internal.py main.py scientific.py -- September 26, 2008 - 17:35

Author: bugman
Date: Fri Sep 26 17:35:58 2008
New Revision: 7350

URL: http://svn.gna.org/viewcvs/relax?rev=7350&view=rev
Log:
Modified the structural object code to store the file name and path.

This will cause some breakages do to the variable name changes.


Modified:
    1.3/generic_fns/structure/api_base.py
    1.3/generic_fns/structure/internal.py
    1.3/generic_fns/structure/main.py
    1.3/generic_fns/structure/scientific.py

Modified: 1.3/generic_fns/structure/api_base.py
URL: 
http://svn.gna.org/viewcvs/relax/1.3/generic_fns/structure/api_base.py?rev=7350&r1=7349&r2=7350&view=diff
==============================================================================
--- 1.3/generic_fns/structure/api_base.py (original)
+++ 1.3/generic_fns/structure/api_base.py Fri Sep 26 17:35:58 2008
@@ -52,8 +52,9 @@
         # The parser specific data object.
         self.structural_data = []
 
-        # Initialise the file name list.
-        self.file_name = []
+        # Initialise the file name and path list.
+        self.file = []
+        self.path = []
 
 
     def atom_add(self, pdb_record=None, atom_num=None, atom_name=None, 
res_name=None, chain_id=None, res_num=None, pos=[None, None, None], 
segment_id=None, element=None, struct_index=None):
@@ -224,7 +225,7 @@
         xml_to_object(str_node, self)
 
         # Now load the structure from file again.
-        self.load_pdb(file_path=self.file_name, model=None)
+        self.load_pdb(file_path=self.file, model=None)
 
 
     def load_pdb(self, file_path, model=None, verbosity=False):

Modified: 1.3/generic_fns/structure/internal.py
URL: 
http://svn.gna.org/viewcvs/relax/1.3/generic_fns/structure/internal.py?rev=7350&r1=7349&r2=7350&view=diff
==============================================================================
--- 1.3/generic_fns/structure/internal.py (original)
+++ 1.3/generic_fns/structure/internal.py Fri Sep 26 17:35:58 2008
@@ -784,15 +784,12 @@
         if verbosity:
             print "Internal relax PDB parser.\n"
 
-        # Store the file name (with full path).
-        self.file_name.append(file_path)
-
         # Use pointers (references) if the PDB data exists in another pipe.
         for data_pipe in ds:
             if hasattr(data_pipe, 'structure'):
                 # Loop over the structures.
                 for i in xrange(len(data_pipe.structure)):
-                    if data_pipe.structure.file_name[i] == file_path and 
data_pipe.structure[i].model == model and data_pipe.structure.id == 
'internal':
+                    if data_pipe.structure.file[i] == file_path and 
data_pipe.structure[i].model == model and data_pipe.structure.id == 
'internal':
                         # Make a pointer to the data.
                         self.structural_data = 
data_pipe.structure.structural_data[i]
 

Modified: 1.3/generic_fns/structure/main.py
URL: 
http://svn.gna.org/viewcvs/relax/1.3/generic_fns/structure/main.py?rev=7350&r1=7349&r2=7350&view=diff
==============================================================================
--- 1.3/generic_fns/structure/main.py (original)
+++ 1.3/generic_fns/structure/main.py Fri Sep 26 17:35:58 2008
@@ -23,7 +23,7 @@
 # Python module imports.
 from math import sqrt
 from numpy import dot, float64, ndarray, zeros
-from os import F_OK, access
+from os import F_OK, access, path
 from re import search
 import sys
 from warnings import warn
@@ -198,6 +198,11 @@
         elif parser == 'internal':
             cdp.structure = Internal()
 
+    # Set the file name and path.
+    expanded = path.split(file_path)
+    cdp.structure.path.append(expanded[0])
+    cdp.structure.file.append(expanded[1])
+
     # Load the structures.
     cdp.structure.load_pdb(file_path, model, verbosity)
 

Modified: 1.3/generic_fns/structure/scientific.py
URL: 
http://svn.gna.org/viewcvs/relax/1.3/generic_fns/structure/scientific.py?rev=7350&r1=7349&r2=7350&view=diff
==============================================================================
--- 1.3/generic_fns/structure/scientific.py (original)
+++ 1.3/generic_fns/structure/scientific.py Fri Sep 26 17:35:58 2008
@@ -477,15 +477,12 @@
         if verbosity:
             print "Scientific Python PDB parser.\n"
 
-        # Store the file name (with full path).
-        self.file_name = file_path
-
         # Store the model number.
         self.model = model
 
         # Use pointers (references) if the PDB data exists in another run.
         for data_pipe in ds:
-            if hasattr(data_pipe, 'structure') and 
data_pipe.structure.file_name == file_path and data_pipe.structure.model == 
model:
+            if hasattr(data_pipe, 'structure') and 
data_pipe.structure.file[0] == file_path and data_pipe.structure.model == 
model:
                 # Make a pointer to the data.
                 self.structural_data = data_pipe.structure.structural_data