Author: bugman
Date: Sat Feb 19 14:41:53 2011
New Revision: 12580
URL: http://svn.gna.org/viewcvs/relax?rev=12580&view=rev
Log:
Merged revisions 8392-8393,8427,8567-8573 via svnmerge from
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/branches/bmrb
........
r8392 | bugman | 2009-01-11 19:05:40 +0100 (Sun, 11 Jan 2009) | 5 lines
Started to dump the relaxation data into the BMRB file.
Much work is still required and the spin specific values are still not
there.
........
r8393 | bugman | 2009-01-11 19:22:44 +0100 (Sun, 11 Jan 2009) | 3 lines
The spectrometer frequency in the BMRB is now a float.
........
r8427 | bugman | 2009-01-12 22:20:30 +0100 (Mon, 12 Jan 2009) | 3 lines
All relaxation data is now placed in the BMRB STAR formatted file.
........
r8567 | bugman | 2009-01-21 21:02:14 +0100 (Wed, 21 Jan 2009) | 6 lines
Added a directory for the creation of the 'bmrb' package.
This will include translation tables of the various BMRB NMR-STAR format
version, and many BMRB
format related functions.
........
r8568 | bugman | 2009-01-21 21:03:14 +0100 (Wed, 21 Jan 2009) | 3 lines
Converted generic_fns.bmrb into the bmrb package initialisation module.
........
r8569 | bugman | 2009-01-21 21:03:42 +0100 (Wed, 21 Jan 2009) | 3 lines
Copyright update.
........
r8570 | bugman | 2009-01-21 21:04:50 +0100 (Wed, 21 Jan 2009) | 3 lines
Updated the module docstring and added an empty __all__ list.
........
r8571 | bugman | 2009-01-21 21:06:37 +0100 (Wed, 21 Jan 2009) | 3 lines
Import fix and copyright update.
........
r8572 | bugman | 2009-01-21 21:17:17 +0100 (Wed, 21 Jan 2009) | 5 lines
Renamed the bmrb package to bmrblib.
This is to avoid any future (and current) name clashes.
........
r8573 | bugman | 2009-01-21 21:18:35 +0100 (Wed, 21 Jan 2009) | 3 lines
Updates for the renaming to bmrblib.
........
Added:
1.3/bmrblib/
- copied from r8573, branches/bmrb/bmrblib/
Removed:
1.3/generic_fns/bmrb.py
Modified:
1.3/ (props changed)
1.3/prompt/bmrb.py
1.3/specific_fns/model_free/bmrb.py
Propchange: 1.3/
------------------------------------------------------------------------------
--- svnmerge-integrated (original)
+++ svnmerge-integrated Sat Feb 19 14:41:53 2011
@@ -1,1 +1,1 @@
-/branches/bmrb:1-7041,7043-7046,8153-8388
+/branches/bmrb:1-7041,7043-7046,8153-8388,8392-8573
Removed: 1.3/generic_fns/bmrb.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/generic_fns/bmrb.py?rev=12579&view=auto
==============================================================================
--- 1.3/generic_fns/bmrb.py (original)
+++ 1.3/generic_fns/bmrb.py (removed)
@@ -1,103 +1,0 @@
-###############################################################################
-#
#
-# Copyright (C) 2008 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.
-"""Module for interfacing with the BMRB (http://www.bmrb.wisc.edu/) by
handling NMR-STAR v3.1 files."""
-
-# Python module imports.
-from os import F_OK, access
-
-# relax module imports.
-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
-
-
-def display():
- """Display the results in the BMRB NMR-STAR v3.1 format."""
-
- # Test if the current data pipe exists.
- if not ds.current_pipe:
- raise RelaxNoPipeError
-
- # Specific results writing function.
- write_function = get_specific_fn('bmrb_write',
ds[ds.current_pipe].pipe_type, raise_error=False)
-
- # Write the results.
- write_function(sys.stdout)
-
-
-def read(file=None, directory=None):
- """Read the contents of a BMRB NMR-STAR v3.1 formatted file."""
-
- # Test if the current data pipe exists.
- if not ds.current_pipe:
- raise RelaxNoPipeError
-
- # Make sure that the data pipe is empty.
- if not ds[ds.current_pipe].is_empty():
- raise RelaxError, "The current data pipe is not empty."
-
- # Get the full file path.
- file_path = get_file_path(file_name=file, dir=directory)
-
- # Fail if the file does not exist.
- if not access(file_path, F_OK):
- raise RelaxFileError, file_path
-
- # Specific results reading function.
- read_function = get_specific_fn('bmrb_read',
ds[ds.current_pipe].pipe_type)
-
- # Read the results.
- read_function(file_path)
-
-
-def write(file=None, directory=None, force=False):
- """Create a BMRB NMR-STAR v3.1 formatted file."""
-
- # Test if the current data pipe exists.
- if not ds.current_pipe:
- raise RelaxNoPipeError
-
- # The special data pipe name directory.
- if directory == 'pipe_name':
- directory = ds.current_pipe
-
- # Specific results writing function.
- write_function = get_specific_fn('bmrb_write',
ds[ds.current_pipe].pipe_type)
-
- # Get the full file path.
- file_path = get_file_path(file, directory)
-
- # Fail if the file already exists and the force flag is False.
- if access(file_path, F_OK) and not force:
- raise RelaxFileOverwriteError, (file_path, 'force flag')
-
- # Print out.
- print "Opening the file '%s' for writing." % file_path
-
- # Create the directories.
- mkdir_nofail(directory, verbosity=0)
-
- # Execute the specific BMRB writing code.
- write_function(file_path)
Modified: 1.3/prompt/bmrb.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/prompt/bmrb.py?rev=12580&r1=12579&r2=12580&view=diff
==============================================================================
--- 1.3/prompt/bmrb.py (original)
+++ 1.3/prompt/bmrb.py Sat Feb 19 14:41:53 2011
@@ -1,6 +1,6 @@
###############################################################################
#
#
-# Copyright (C) 2003-2005,2008 Edward d'Auvergne
#
+# Copyright (C) 2003-2005,2008-2009 Edward d'Auvergne
#
#
#
# This file is part of the program relax.
#
#
#
@@ -25,7 +25,7 @@
# relax module imports.
import help
-from generic_fns import bmrb
+import bmrblib
from relax_errors import RelaxBoolError, RelaxIntError, RelaxNoneStrError,
RelaxStrError, RelaxStrFileError
@@ -52,7 +52,7 @@
print text
# Execute the functional code.
- bmrb.display(format=format)
+ bmrblib.display(format=format)
def read(self, file=None, dir=None):
@@ -88,7 +88,7 @@
raise RelaxNoneStrError, ('directory name', dir)
# Execute the functional code.
- bmrb.read(file=file, directory=dir)
+ bmrblib.read(file=file, directory=dir)
def write(self, file=None, dir='pipe_name', force=False):
@@ -134,4 +134,4 @@
raise RelaxBoolError, ('force flag', force)
# Execute the functional code.
- bmrb.write(file=file, directory=dir, force=force)
+ bmrblib.write(file=file, directory=dir, force=force)
Modified: 1.3/specific_fns/model_free/bmrb.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/specific_fns/model_free/bmrb.py?rev=12580&r1=12579&r2=12580&view=diff
==============================================================================
--- 1.3/specific_fns/model_free/bmrb.py (original)
+++ 1.3/specific_fns/model_free/bmrb.py Sat Feb 19 14:41:53 2011
@@ -21,7 +21,11 @@
###############################################################################
# relax module imports.
+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
class Bmrb:
@@ -51,5 +55,83 @@
# Initialise the pystarlib File object.
file = File(title='relax_model_free_results', filename=file_path)
+ # Get the current data pipe.
+ cdp = get_pipe()
+
+ # Initialise the spin specific data lists.
+ res_num_list = []
+ res_name_list = []
+ atom_name_list = []
+ relax_data_list = []
+ relax_error_list = []
+ for i in range(cdp.num_ri):
+ relax_data_list.append([])
+ relax_error_list.append([])
+
+ # Store the spin specific data in lists for later use.
+ for spin, mol_name, res_num, res_name in spin_loop(full_info=True):
+ # Skip deselected spins.
+ if not spin.select:
+ continue
+
+ # The residue/spin info.
+ res_num_list.append(str(res_num))
+ res_name_list.append(str(res_name))
+ atom_name_list.append(str(spin.name))
+
+ # The relaxation data.
+ for i in range(cdp.num_ri):
+ relax_data_list[i].append(str(spin.relax_data[i]))
+ relax_error_list[i].append(str(spin.relax_error[i]))
+
+ # Relaxation data save frames.
+ r1_inc = 0
+ r2_inc = 0
+ noe_inc = 0
+ for i in range(cdp.num_ri):
+ # Data type labels.
+ if cdp.ri_labels[i] == 'R1':
+ r1_inc = r1_inc + 1
+ ri_inc = r1_inc
+ ri_label = 'T1'
+ coherence = 'Nz'
+ elif cdp.ri_labels[i] == 'R2':
+ r2_inc = r2_inc + 1
+ ri_inc = r2_inc
+ ri_label = 'T2'
+ coherence = 'Ny'
+ elif cdp.ri_labels[i] == 'NOE':
+ noe_inc = noe_inc + 1
+ ri_inc = noe_inc
+ ri_label = 'NOE'
+
+ # Initialise the save frame.
+ frame =
SaveFrame(title='heteronuclear_'+ri_label+'_list_'+`ri_inc`)
+
+ # The save frame category.
+ frame.tagtables.append(TagTable(free=True,
tagnames=['_Saveframe_category'], tagvalues=[[ri_label+'_relaxation']]))
+
+ # Sample info.
+ frame.tagtables.append(TagTable(free=True,
tagnames=['_Sample_label'], tagvalues=[['$sample_1']]))
+ frame.tagtables.append(TagTable(free=True,
tagnames=['_Sample_conditions_label'], tagvalues=[['$conditions_1']]))
+
+ # NMR info.
+ frame.tagtables.append(TagTable(free=True,
tagnames=['_Spectrometer_frequency_1H'],
tagvalues=[[str(cdp.frq[cdp.remap_table[i]]/1e6)]]))
+ if ri_label in ['T1', 'T2']:
+ frame.tagtables.append(TagTable(free=True,
tagnames=['_'+ri_label+'_coherence_type'], tagvalues=[[coherence]]))
+ frame.tagtables.append(TagTable(free=True,
tagnames=['_'+ri_label+'_value_units'], tagvalues=[['1/s']]))
+
+ # The relaxation tag names.
+ tag_names = ['_Residue_seq_code', '_Residue_label',
'_Atom_name', '_'+ri_label+'_value', '_'+ri_label+'_value_error']
+
+ # Add the data.
+ table = TagTable(tagnames=tag_names, tagvalues=[res_num_list,
res_name_list, atom_name_list, relax_data_list[i], relax_error_list[i]])
+
+ # Add the tag table to the save frame.
+ frame.tagtables.append(table)
+
+ # Add the relaxation data save frame.
+ file.datanodes.append(frame)
+
# Write the contents to the STAR formatted file.
file.write()
r12580 - in /1.3: ./ bmrblib/ generic_fns/bmrb.py prompt/bmrb.py specific_fns/model_free/bmrb.py