Author: bugman
Date: Sat Feb 21 23:50:56 2009
New Revision: 8834
URL: http://svn.gna.org/viewcvs/relax?rev=8834&view=rev
Log:
Started to create the NMR-STAR dictionary object.
The object is in bmrblib.nmr_star_dict and acts as an abstraction layer
between pystarlib and the
specific analysis types. It also will translate the NMR-STAR dictionary
subset used by relax for
different versions of the definition. The object is far from complete though.
Added:
branches/bmrb/bmrblib/nmr_star_dict.py
Modified:
branches/bmrb/bmrblib/__init__.py
branches/bmrb/specific_fns/model_free/bmrb.py
Modified: branches/bmrb/bmrblib/__init__.py
URL:
http://svn.gna.org/viewcvs/relax/branches/bmrb/bmrblib/__init__.py?rev=8834&r1=8833&r2=8834&view=diff
==============================================================================
--- branches/bmrb/bmrblib/__init__.py (original)
+++ branches/bmrb/bmrblib/__init__.py Sat Feb 21 23:50:56 2009
@@ -30,10 +30,10 @@
from data import Relax_data_store; ds = Relax_data_store()
from relax_errors import RelaxError, RelaxFileError,
RelaxFileOverwriteError, RelaxNoPipeError
from relax_io import get_file_path, mkdir_nofail
-from specific_fns.setup import get_specific_fn
+import specific_fns
-__all__ = []
+__all__ = ['nmr_star_dict']
@@ -45,7 +45,7 @@
raise RelaxNoPipeError
# Specific results writing function.
- write_function = get_specific_fn('bmrb_write',
ds[ds.current_pipe].pipe_type, raise_error=False)
+ write_function = specific_fns.setup.get_specific_fn('bmrb_write',
ds[ds.current_pipe].pipe_type, raise_error=False)
# Write the results.
write_function(sys.stdout)
@@ -70,7 +70,7 @@
raise RelaxFileError, file_path
# Specific results reading function.
- read_function = get_specific_fn('bmrb_read',
ds[ds.current_pipe].pipe_type)
+ read_function = specific_fns.setup.get_specific_fn('bmrb_read',
ds[ds.current_pipe].pipe_type)
# Read the results.
read_function(file_path)
@@ -88,7 +88,7 @@
directory = ds.current_pipe
# Specific results writing function.
- write_function = get_specific_fn('bmrb_write',
ds[ds.current_pipe].pipe_type)
+ write_function = specific_fns.setup.get_specific_fn('bmrb_write',
ds[ds.current_pipe].pipe_type)
# Get the full file path.
file_path = get_file_path(file, directory)
Added: branches/bmrb/bmrblib/nmr_star_dict.py
URL:
http://svn.gna.org/viewcvs/relax/branches/bmrb/bmrblib/nmr_star_dict.py?rev=8834&view=auto
==============================================================================
--- branches/bmrb/bmrblib/nmr_star_dict.py (added)
+++ branches/bmrb/bmrblib/nmr_star_dict.py Sat Feb 21 23:50:56 2009
@@ -1,0 +1,60 @@
+###############################################################################
+#
#
+# Copyright (C) 2009 Edward d'Auvergne
#
+#
#
+# This file is part of the program relax.
#
+#
#
+# relax is free software; you can redistribute it and/or modify
#
+# it under the terms of the GNU General Public License as published by
#
+# the Free Software Foundation; either version 2 of the License, or
#
+# (at your option) any later version.
#
+#
#
+# relax is distributed in the hope that it will be useful,
#
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
#
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
#
+# GNU General Public License for more details.
#
+#
#
+# You should have received a copy of the GNU General Public License
#
+# along with relax; if not, write to the Free Software
#
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
#
+#
#
+###############################################################################
+
+# Module docstring.
+"""The base classes for the NMR-STAR dictionary support within relax.
+
+The most up to date NMR-STAR dictionary relax uses is the v3.1 version
documented at
+http://www.bmrb.wisc.edu/dictionary/3.1html/SuperGroupPage.html.
+"""
+
+# relax module imports.
+from pystarlib.File import File
+
+
+class NMR_STAR:
+ """The base object for the NMR-STAR dictionary."""
+
+ def __init__(self, title, file_path):
+ """Initialise the NMR-STAR dictionary object.
+
+ @param title: The title of the NMR-STAR data.
+ @type title: str
+ @param file_path: The full file path.
+ @type file_path: str
+ """
+
+ # Initialise the pystarlib File object.
+ self.file = File(title='relax_model_free_results',
filename=file_path)
+
+
+ def read(self):
+ """Read the data from a BMRB NMR-STAR formatted file."""
+
+ self.file.read()
+
+
+ def write(self):
+ """Write the data to a BMRB NMR-STAR formatted file."""
+
+ # Write the contents to the STAR formatted file.
+ self.file.write()
Modified: branches/bmrb/specific_fns/model_free/bmrb.py
URL:
http://svn.gna.org/viewcvs/relax/branches/bmrb/specific_fns/model_free/bmrb.py?rev=8834&r1=8833&r2=8834&view=diff
==============================================================================
--- branches/bmrb/specific_fns/model_free/bmrb.py (original)
+++ branches/bmrb/specific_fns/model_free/bmrb.py Sat Feb 21 23:50:56 2009
@@ -21,9 +21,9 @@
###############################################################################
# relax module imports.
+from bmrblib.nmr_star_dict import NMR_STAR
from generic_fns.mol_res_spin import spin_loop
from generic_fns.pipes import get_pipe
-from pystarlib.File import File
from pystarlib.SaveFrame import SaveFrame
from pystarlib.TagTable import TagTable
@@ -38,11 +38,11 @@
@type file_path: str
"""
- # Initialise the pystarlib File object.
- file = File(title='relax_model_free_results', filename=file_path)
+ # Initialise the NMR-STAR data object.
+ star = NMR_STAR('relax_model_free_results', file_path)
# Read the contents of the STAR formatted file.
- file.read()
+ star.read()
def bmrb_write(self, file_path):
@@ -52,8 +52,8 @@
@type file_path: str
"""
- # Initialise the pystarlib File object.
- file = File(title='relax_model_free_results', filename=file_path)
+ # Initialise the NMR-STAR data object.
+ star = NMR_STAR('relax_model_free_results', file_path)
# Get the current data pipe.
cdp = get_pipe()
@@ -131,7 +131,7 @@
frame.tagtables.append(table)
# Add the relaxation data save frame.
- file.datanodes.append(frame)
+ star.file.datanodes.append(frame)
# Write the contents to the STAR formatted file.
- file.write()
+ star.write()
r8834 - in /branches/bmrb: bmrblib/__init__.py bmrblib/nmr_star_dict.py specific_fns/model_free/bmrb.py