r18019 - in /branches/frame_order_testing/generic_fns/structure: internal.py scientific.py -- November 22, 2012 - 11:48

Author: bugman
Date: Thu Nov 22 11:48:15 2012
New Revision: 18019

URL: http://svn.gna.org/viewcvs/relax?rev=18019&view=rev
Log:
The absolute path to PDB and XYZ 3D structure files is now kept in the relax 
data store.

This is for both the internal PDB and XYZ reader, and the Scientific Python 
PDB reader.


Modified:
    branches/frame_order_testing/generic_fns/structure/internal.py
    branches/frame_order_testing/generic_fns/structure/scientific.py

Modified: branches/frame_order_testing/generic_fns/structure/internal.py
URL: 
http://svn.gna.org/viewcvs/relax/branches/frame_order_testing/generic_fns/structure/internal.py?rev=18019&r1=18018&r2=18019&view=diff
==============================================================================
--- branches/frame_order_testing/generic_fns/structure/internal.py (original)
+++ branches/frame_order_testing/generic_fns/structure/internal.py Thu Nov 22 
11:48:15 2012
@@ -25,7 +25,8 @@
 # Python module imports.
 from numpy import array, dot, float64, linalg, zeros
 import os
-from os import F_OK, access
+from os import F_OK, access, curdir, sep
+from os.path import abspath
 from re import search
 from string import digits
 from warnings import warn
@@ -1067,6 +1068,9 @@
         # Separate the file name and path.
         path, file = os.path.split(file_path)
 
+        # The absolute path.
+        path_abs = abspath(curdir) + sep + path
+
         # Convert the structure reading args into lists.
         if read_mol and not isinstance(read_mol, list):
             read_mol = [read_mol]
@@ -1136,7 +1140,7 @@
             return False
 
         # Create the structural data data structures.
-        self.pack_structs(mol_conts, orig_model_num=orig_model_num, 
set_model_num=set_model_num, orig_mol_num=orig_mol_num, 
set_mol_name=new_mol_name, file_name=file, file_path=path)
+        self.pack_structs(mol_conts, orig_model_num=orig_model_num, 
set_model_num=set_model_num, orig_mol_num=orig_mol_num, 
set_mol_name=new_mol_name, file_name=file, file_path=path, 
file_path_abs=path_abs)
 
         # Loading worked.
         return True
@@ -1180,6 +1184,9 @@
         # Separate the file name and path.
         path, file = os.path.split(file_path)
 
+        # The absolute path.
+        path_abs = abspath(curdir) + sep + path
+
         # Convert the structure reading args into lists.
         if read_mol and not isinstance(read_mol, list):
             read_mol = [read_mol]
@@ -1242,7 +1249,7 @@
 
         orig_mol_num=[0]
         # Create the structural data data structures.
-        self.pack_structs(mol_conts, orig_model_num=orig_model_num, 
set_model_num=set_model_num, orig_mol_num=orig_mol_num, 
set_mol_name=new_mol_name, file_name=file, file_path=path)
+        self.pack_structs(mol_conts, orig_model_num=orig_model_num, 
set_model_num=set_model_num, orig_mol_num=orig_mol_num, 
set_mol_name=new_mol_name, file_name=file, file_path=path, 
file_path_abs=path_abs)
 
         # Loading worked.
         return True

Modified: branches/frame_order_testing/generic_fns/structure/scientific.py
URL: 
http://svn.gna.org/viewcvs/relax/branches/frame_order_testing/generic_fns/structure/scientific.py?rev=18019&r1=18018&r2=18019&view=diff
==============================================================================
--- branches/frame_order_testing/generic_fns/structure/scientific.py 
(original)
+++ branches/frame_order_testing/generic_fns/structure/scientific.py Thu Nov 
22 11:48:15 2012
@@ -29,7 +29,8 @@
 from math import sqrt
 from numpy import array, dot, float64, linalg, zeros
 import os
-from os import F_OK, access, sep
+from os import F_OK, access, curdir, sep
+from os.path import abspath
 from extern.scientific_python.IO import PDB
 import sys
 from warnings import warn
@@ -593,6 +594,9 @@
         # Separate the file name and path.
         path, file = os.path.split(file_path)
 
+        # The absolute path.
+        path_abs = abspath(curdir) + sep + path
+
         # Convert the structure reading args into lists.
         if read_mol and not isinstance(read_mol, list):
             read_mol = [read_mol]
@@ -720,7 +724,7 @@
             model_load_num = model_load_num + 1
 
         # Create the structural data data structures.
-        self.pack_structs(mol_conts, orig_model_num=orig_model_num, 
set_model_num=set_model_num, orig_mol_num=list(range(1, 
len(mol_conts[0])+1)), set_mol_name=new_mol_name, file_name=file, 
file_path=path)
+        self.pack_structs(mol_conts, orig_model_num=orig_model_num, 
set_model_num=set_model_num, orig_mol_num=list(range(1, 
len(mol_conts[0])+1)), set_mol_name=new_mol_name, file_name=file, 
file_path=path, file_path_abs=path_abs)
 
         # Loading worked.
         return True