Author: bugman
Date: Sun Oct 11 15:41:56 2009
New Revision: 9721
URL: http://svn.gna.org/viewcvs/relax?rev=9721&view=rev
Log:
Created the bmrb.software() user function for manually specifying the
software used.
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=9721&r1=9720&r2=9721&view=diff
==============================================================================
--- branches/bmrb/generic_fns/bmrb.py (original)
+++ branches/bmrb/generic_fns/bmrb.py Sun Oct 11 15:41:56 2009
@@ -73,6 +73,31 @@
read_function(file_path, version=version)
+def software(name=None, version=None, url=None, vendor_name=None, cite=None,
tasks=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: None or str
+ @keyword url: The program's URL.
+ @type url: None or str
+ @keyword vendor_name: The name of the company or person behind the
program.
+ @type vendor_name: str
+ @keyword cite: The literature citation.
+ @type cite: None or str
+ @keyword tasks: The tasks performed by the program.
+ @type tasks: list of str
+ """
+
+ # Set up the experimental info data container, if needed.
+ if not hasattr(cdp, 'exp_info'):
+ cdp.exp_info = ExpInfo()
+
+ # Place the data in the container.
+ cdp.exp_info.software_setup(name=name, version=version, url=url,
vendor_name=vendor_name, cite=cite, tasks=tasks)
+
+
def software_select(name, version=None):
"""Select by name the software used in the analysis.
Modified: branches/bmrb/prompt/bmrb.py
URL:
http://svn.gna.org/viewcvs/relax/branches/bmrb/prompt/bmrb.py?rev=9721&r1=9720&r2=9721&view=diff
==============================================================================
--- branches/bmrb/prompt/bmrb.py (original)
+++ branches/bmrb/prompt/bmrb.py Sun Oct 11 15:41:56 2009
@@ -84,6 +84,78 @@
bmrb.read(file=file, directory=dir, version=version)
+ def software(self, name=None, version=None, url=None, vendor_name=None,
cite=None, tasks=None):
+ """Specify the software used in the analysis.
+
+ Keyword Arguments
+ ~~~~~~~~~~~~~~~~~
+
+ name: The name of the software program utilised.
+
+ version: The version of the software, if applicable.
+
+ url: The web address of the software.
+
+ vendor_name: The name of the company or person behind the program.
+
+ cite: The literature citation for the software.
+
+ tasks: A list of all the tasks performed by the software.
+
+
+ Description
+ ~~~~~~~~~~~
+
+ This user function allows the software used in the analysis to be
specified in full detail.
+
+ For the tasks list, this should be a python list of strings (eg.
['spectral processing']).
+ Although not restricted to these, the values suggested by the BMRB
are:
+
+ 'chemical shift assignment',
+ 'chemical shift calculation',
+ 'collection',
+ 'data analysis',
+ 'geometry optimization',
+ 'peak picking',
+ 'processing',
+ 'refinement',
+ 'structure solution'
+
+
+ Examples
+ ~~~~~~~~
+
+ For BMRB deposition, to say that Sparky was used in the analysis,
type:
+
+ relax> bmrb.software('Sparky', version='3.110',
url="http://www.cgl.ucsf.edu/home/sparky/";,
+ vendor_name="Goddard, T. D.", cite="Goddard, T.
D. and Kneller, D. G.,
+ SPARKY 3, University of California, San
Francisco.",
+ tasks=["spectral analysis"])
+ """
+
+ # Function intro text.
+ if self.__relax__.interpreter.intro:
+ text = sys.ps3 + "bmrb.software_select("
+ text = text + "name=" + repr(name)
+ text = text + ", version=" + repr(version)
+ text = text + ", url=" + repr(url)
+ text = text + ", vendor_name=" + repr(vendor_name)
+ text = text + ", cite=" + repr(cite)
+ text = text + ", tasks=" + repr(tasks) + ")"
+ print(text)
+
+ # The argument checks.
+ check.is_str(name, 'program name')
+ check.is_str(version, 'version', can_be_none=True)
+ check.is_str(url, 'url', can_be_none=True)
+ check.is_str(vendor_name, 'vendor_name', can_be_none=True)
+ check.is_str(cite, 'cite', can_be_none=True)
+ check.is_str_list(tasks, 'tasks', can_be_none=True)
+
+ # Execute the functional code.
+ bmrb.software(name=name, version=version, url=url,
vendor_name=vendor_name, cite=cite, tasks=tasks)
+
+
def software_select(self, name=None, version=None):
"""Select the software used in the analysis.
@@ -91,6 +163,8 @@
~~~~~~~~~~~~~~~~~
name: The name of the software program utilised.
+
+ version: The version of the software, if applicable.
Description
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=9721&r1=9720&r2=9721&view=diff
==============================================================================
--- branches/bmrb/test_suite/system_tests/scripts/bmrb_rw.py (original)
+++ branches/bmrb/test_suite/system_tests/scripts/bmrb_rw.py Sun Oct 11
15:41:56 2009
@@ -36,6 +36,7 @@
# Set up all the BMRB information.
bmrb.software_select('NMRPipe')
bmrb.software_select('Sparky', version='3.106')
+bmrb.software(name='X', url='http://X.X.X', vendor_name='me',
cite='Nothing!', tasks=['procrastinating', 'nothing much', 'wasting time'])
# Write, then read the data to a new data pipe.
bmrb.write(file=ds.tmpfile, dir=None, version=ds.version, force=True)
r9721 - in /branches/bmrb: generic_fns/bmrb.py prompt/bmrb.py test_suite/system_tests/scripts/bmrb_rw.py