r9712 - in /branches/bmrb: generic_fns/bmrb.py prompt/bmrb.py test_suite/system_tests/scripts/bmrb_rw.py -- October 09, 2009 - 20:25

Author: bugman
Date: Fri Oct  9 20:25:00 2009
New Revision: 9712

URL: http://svn.gna.org/viewcvs/relax?rev=9712&view=rev
Log:
Created the user function bmrb.software_select().

This currently doesn't do anything.


Modified:
    branches/bmrb/generic_fns/bmrb.py
    branches/bmrb/prompt/bmrb.py
    branches/bmrb/test_suite/system_tests/scripts/bmrb_rw.py

Modified: branches/bmrb/generic_fns/bmrb.py
URL: 
http://svn.gna.org/viewcvs/relax/branches/bmrb/generic_fns/bmrb.py?rev=9712&r1=9711&r2=9712&view=diff
==============================================================================
--- branches/bmrb/generic_fns/bmrb.py (original)
+++ branches/bmrb/generic_fns/bmrb.py Fri Oct  9 20:25:00 2009
@@ -72,6 +72,32 @@
     read_function(file_path, version=version)
 
 
+def software_select(name, version=None):
+    """Select by name the software used in the analysis.
+
+    @param name:        The name of the software program.
+    @type name:         str
+    @keyword version:   The program version.
+    @type version:      str
+    """
+
+    # NMRPipe.
+    if name == 'NMRPipe':
+        pass
+
+    # Sparky.
+    elif name == 'Sparky':
+        # Check if the version information has been supplied.
+        if not version:
+            raise RelaxError("The Sparky version number has not been 
supplied.")
+
+        # The data.
+
+    # Unknown program.
+    else:
+        raise RelaxError("The software '%s' is unknown.  Please use the user 
function for manually specifying software details instead." % name)
+
+
 def write(file=None, directory=None, version='3.1', force=False):
     """Create a BMRB NMR-STAR formatted file."""
 

Modified: branches/bmrb/prompt/bmrb.py
URL: 
http://svn.gna.org/viewcvs/relax/branches/bmrb/prompt/bmrb.py?rev=9712&r1=9711&r2=9712&view=diff
==============================================================================
--- branches/bmrb/prompt/bmrb.py (original)
+++ branches/bmrb/prompt/bmrb.py Fri Oct  9 20:25:00 2009
@@ -84,6 +84,54 @@
         bmrb.read(file=file, directory=dir, version=version)
 
 
+    def software_select(self, name=None, version=None):
+        """Select the software used in the analysis.
+
+        Keyword Arguments
+        ~~~~~~~~~~~~~~~~~
+
+        name:  The name of the software program utilised.
+
+
+        Description
+        ~~~~~~~~~~~
+
+        Rather than specifying all the information directly, this user 
function allows the software
+        packaged used in the analysis to be selected by name.  The programs 
currently supported are:
+
+            'NMRPipe' - http://spin.niddk.nih.gov/NMRPipe/
+            'Sparky' - http://www.cgl.ucsf.edu/home/sparky/
+
+        More can be added if all relevant information (program name, 
description, website, original
+        citation, purpose, etc.) is emailed to relax-users@xxxxxxxx
+
+        Note that relax is automatically added to the BMRB file.
+
+
+        Examples
+        ~~~~~~~~
+
+        For BMRB deposition, to say that both NMRPipe and Sparky were used 
prior to relax, type:
+
+        relax> bmrb.software_select('NMRPipe')
+        relax> bmrb.software_select('Sparky', version='3.113')
+        """
+
+        # Function intro text.
+        if self.__relax__.interpreter.intro:
+            text = sys.ps3 + "bmrb.software_select("
+            text = text + "name=" + repr(name)
+            text = text + ", version=" + repr(version) + ")"
+            print(text)
+
+        # The argument checks.
+        check.is_str(name, 'program name')
+        check.is_str(version, 'version', can_be_none=True)
+
+        # Execute the functional code.
+        bmrb.software_select(name=name, version=version)
+
+
     def write(self, file=None, dir='pipe_name', version='3.1', force=False):
         """Write the results to a BMRB NMR-STAR formatted file.
 

Modified: branches/bmrb/test_suite/system_tests/scripts/bmrb_rw.py
URL: 
http://svn.gna.org/viewcvs/relax/branches/bmrb/test_suite/system_tests/scripts/bmrb_rw.py?rev=9712&r1=9711&r2=9712&view=diff
==============================================================================
--- branches/bmrb/test_suite/system_tests/scripts/bmrb_rw.py (original)
+++ branches/bmrb/test_suite/system_tests/scripts/bmrb_rw.py Fri Oct  9 
20:25:00 2009
@@ -33,6 +33,10 @@
 # Display the data (as a test).
 relax_data.display(ri_label='R1', frq_label='800')
 
+# Set up all the BMRB information.
+bmrb.software_select('NMRPipe')
+bmrb.software_select('Sparky', version='3.106')
+
 # Write, then read the data to a new data pipe.
 bmrb.write(file=ds.tmpfile, dir=None, version=ds.version, force=True)
 pipe.create(pipe_name='new', pipe_type='mf')