r14898 - in /1.3: generic_fns/structure/main.py prompt/structure.py -- October 24, 2011 - 15:01

Author: bugman
Date: Mon Oct 24 15:01:47 2011
New Revision: 14898

URL: http://svn.gna.org/viewcvs/relax?rev=14898&view=rev
Log:
The structure.write_pdb user function can now create compressed (bzip2 or 
gzip) PDB files.


Modified:
    1.3/generic_fns/structure/main.py
    1.3/prompt/structure.py

Modified: 1.3/generic_fns/structure/main.py
URL: 
http://svn.gna.org/viewcvs/relax/1.3/generic_fns/structure/main.py?rev=14898&r1=14897&r2=14898&view=diff
==============================================================================
--- 1.3/generic_fns/structure/main.py (original)
+++ 1.3/generic_fns/structure/main.py Mon Oct 24 15:01:47 2011
@@ -581,7 +581,7 @@
         raise RelaxError("No vectors could be extracted.")
 
 
-def write_pdb(file=None, dir=None, model_num=None, force=False):
+def write_pdb(file=None, dir=None, model_num=None, compress_type=0, 
force=False):
     """The PDB writing function.
 
     @keyword file:          The name of the PDB file to write.
@@ -590,6 +590,8 @@
     @type dir:              str or None
     @keyword model_num:     The model to place into the PDB file.  If not 
supplied, then all models will be placed into the file.
     @type model_num:        None or int
+    @keyword compress_type: The compression type.  The integer values 
correspond to the compression type: 0, no compression; 1, Bzip2 compression; 
2, Gzip compression.
+    @type compress_type:    int
     @keyword force:         The force flag which if True will cause the file 
to be overwritten.
     @type force:            bool
     """
@@ -613,7 +615,7 @@
         file_path = file_path + '.pdb'
 
     # Open the file for writing.
-    file = open_write_file(file_path, force=force)
+    file = open_write_file(file_path, compress_type=compress_type, 
force=force)
 
     # Write the structures.
     cdp.structure.write_pdb(file, model_num=model_num)

Modified: 1.3/prompt/structure.py
URL: 
http://svn.gna.org/viewcvs/relax/1.3/prompt/structure.py?rev=14898&r1=14897&r2=14898&view=diff
==============================================================================
--- 1.3/prompt/structure.py (original)
+++ 1.3/prompt/structure.py Mon Oct 24 15:01:47 2011
@@ -547,13 +547,14 @@
     _build_doc(vectors)
 
 
-    def write_pdb(self, file=None, dir=None, model_num=None, force=False):
+    def write_pdb(self, file=None, dir=None, model_num=None, 
compress_type=0, force=False):
         # Function intro text.
         if self._exec_info.intro:
             text = self._exec_info.ps3 + "structure.write_pdb("
             text = text + "file=" + repr(file)
             text = text + ", dir=" + repr(dir)
             text = text + ", model_num=" + repr(model_num)
+            text = text + ", compress_type=" + repr(compress_type)
             text = text + ", force=" + repr(force) + ")"
             print(text)
 
@@ -561,10 +562,11 @@
         arg_check.is_str(file, 'file name')
         arg_check.is_str(dir, 'directory name', can_be_none=True)
         arg_check.is_int(model_num, 'model number', can_be_none=True)
+        arg_check.is_int(compress_type, 'compression type')
         arg_check.is_bool(force, 'force flag')
 
         # Execute the functional code.
-        generic_fns.structure.main.write_pdb(file=file, dir=dir, 
model_num=model_num, force=force)
+        generic_fns.structure.main.write_pdb(file=file, dir=dir, 
model_num=model_num, compress_type=compress_type, force=force)
 
     # The function doc info.
     write_pdb._doc_title = "Writing structures to a PDB file."
@@ -572,9 +574,16 @@
     write_pdb._doc_args = [["file", "The name of the PDB file."],
                            ["dir", "The directory where the file is 
located."],
                            ["model_num", "Restrict the writing of structural 
data to a single model in the PDB file."],
+                           ["compress_type", "The type of compression to use 
when creating the file."],
                            ["force", "A flag which if set to True will cause 
any pre-existing files to be overwritten."]]
     write_pdb._doc_desc = """
         This will write all of the structural data loaded in the current 
data pipe to be converted to the PDB format and written to file.  Specifying 
the model number allows single models to be output.
+
+        The default behaviour of this function is to not compress the file.  
The compression can, however, be changed to either bzip2 or gzip compression. 
 If the '.bz2' or '.gz' extension is not included in the file name, it will 
be added.  This behaviour is controlled by the compress_type argument which 
can be set to
+
+            0:  No compression (no file extension).
+            1:  bzip2 compression ('.bz2' file extension).
+            2:  gzip compression ('.gz' file extension).
         """
     write_pdb._doc_examples = """
         To write all models and molecules to the PDB file 'ensemble.pdb' 
within the directory '~/pdb', type