Author: bugman
Date: Thu Jul 31 11:29:45 2008
New Revision: 7043
URL: http://svn.gna.org/viewcvs/relax?rev=7043&view=rev
Log:
Initial support for the bmrb user functions.
The following BNMRB related user functions now exist (the back end does not
yet exist):
bmrb.display()
bmrb.read()
bmrb.write()
Added:
branches/bmrb/prompt/bmrb.py
- copied, changed from r7041, branches/bmrb/prompt/results.py
Modified:
branches/bmrb/prompt/__init__.py
Modified: branches/bmrb/prompt/__init__.py
URL:
http://svn.gna.org/viewcvs/relax/branches/bmrb/prompt/__init__.py?rev=7043&r1=7042&r2=7043&view=diff
==============================================================================
--- branches/bmrb/prompt/__init__.py (original)
+++ branches/bmrb/prompt/__init__.py Thu Jul 31 11:29:45 2008
@@ -1,6 +1,6 @@
###############################################################################
#
#
-# Copyright (C) 2003-2005 Edward d'Auvergne
#
+# Copyright (C) 2003-2008 Edward d'Auvergne
#
#
#
# This file is part of the program relax.
#
#
#
@@ -22,6 +22,7 @@
__all__ = ['angles',
+ 'bmrb',
'command',
'consistency_tests',
'dasha',
Copied: branches/bmrb/prompt/bmrb.py (from r7041,
branches/bmrb/prompt/results.py)
URL:
http://svn.gna.org/viewcvs/relax/branches/bmrb/prompt/bmrb.py?p2=branches/bmrb/prompt/bmrb.py&p1=branches/bmrb/prompt/results.py&r1=7041&r2=7043&rev=7043&view=diff
==============================================================================
--- branches/bmrb/prompt/results.py (original)
+++ branches/bmrb/prompt/bmrb.py Thu Jul 31 11:29:45 2008
@@ -25,15 +25,15 @@
# relax module imports.
import help
-from generic_fns import results
+from generic_fns import bmrb
from relax_errors import RelaxBoolError, RelaxIntError, RelaxNoneStrError,
RelaxStrError, RelaxStrFileError
-class Results:
+class BMRB:
def __init__(self, relax):
# Help.
self.__relax_help__ = \
- """Class for manipulating results."""
+ """Class for interfacing with the BMRB
(http://www.bmrb.wisc.edu/)."""
# Add the generic help string.
self.__relax_help__ = self.__relax_help__ + "\n" +
help.relax_class_help
@@ -42,32 +42,26 @@
self.__relax__ = relax
- def display(self, format='xml'):
- """Function for displaying the results.
+ def display(self):
+ """Display the BMRB data in NMR-STAR v3.1 format."""
+
+ # Function intro text.
+ if self.__relax__.interpreter.intro:
+ text = sys.ps3 + "bmrb.display("
+ text = text + "format=" + `format` + ")"
+ print text
+
+ # Execute the functional code.
+ bmrb.display(format=format)
+
+
+ def read(self, file=None, dir=None):
+ """Read BMRB files in the NMR-STAR v3.1 format.
Keyword Arguments
~~~~~~~~~~~~~~~~~
- format: The format of the output.
- """
-
- # Function intro text.
- if self.__relax__.interpreter.intro:
- text = sys.ps3 + "results.display("
- text = text + "format=" + `format` + ")"
- print text
-
- # Execute the functional code.
- results.display(format=format)
-
-
- def read(self, file='results', dir=None):
- """Function for reading results from a file.
-
- Keyword Arguments
- ~~~~~~~~~~~~~~~~~
-
- file: The name of the file to read results from.
+ file: The name of the BMRB STAR formatted file.
dir: The directory where the file is located.
@@ -85,7 +79,7 @@
# Function intro text.
if self.__relax__.interpreter.intro:
- text = sys.ps3 + "results.read("
+ text = sys.ps3 + "bmrb.read("
text = text + "file=" + `file`
text = text + ", dir=" + `dir` + ")"
print text
@@ -99,23 +93,21 @@
raise RelaxNoneStrError, ('directory name', dir)
# Execute the functional code.
- results.read(file=file, directory=dir)
+ bmrb.read(file=file, directory=dir)
- def write(self, file='results', dir='pipe_name', force=False,
format='xml', compress_type=1):
- """Function for writing results to a file.
+ def write(self, file=None, dir='pipe_name', force=False,
compress_type=0):
+ """Write the results to a BMRB NMR-STAR v3.1 formatted file.
Keyword Arguments
~~~~~~~~~~~~~~~~~
- file: The name of the file to output results to. The default is
'results'. Optionally
- this can be a file object, or any object with a write() method.
+ file: The name of the BMRB file to output results to. Optionally
this can be a file
+ object, or any object with a write() method.
dir: The directory name.
- force: A flag which if True will cause the results file to be
overwritten.
-
- format: The format of the output.
+ force: A flag which if True will cause the any pre-existing file to
be overwritten.
compress_type: The type of compression to use when creating the
file.
@@ -123,14 +115,13 @@
Description
~~~~~~~~~~~
- To place the results file in the current working directory, set dir
to None. If dir is set
+ To place the BMRB file in the current working directory, set dir to
None. If dir is set
to the special name 'pipe_name', then the results file will be
placed into a directory with
the same name as the current data pipe.
- The default behaviour of this function is to compress the file using
bzip2 compression. If
- the extension '.bz2' is not included in the file name, it will be
added. The compression
- can, however, be changed to either no compression or gzip
compression. This is controlled
- by the compress_type argument which can be set to
+ The default behaviour of this function is to create an uncompressed
BMRB file. The file can
+ however be saved in compressed format. This is controlled by the
compress_type argument
+ which can be set to one of:
0: No compression (no file extension),
1: bzip2 compression ('.bz2' file extension),
@@ -141,11 +132,10 @@
# Function intro text.
if self.__relax__.interpreter.intro:
- text = sys.ps3 + "results.write("
+ text = sys.ps3 + "bmrb.write("
text = text + "file=" + `file`
text = text + ", dir=" + `dir`
text = text + ", force=" + `force`
- text = text + ", format=" + `format`
text = text + ", compress_type=" + `compress_type` + ")"
print text
@@ -161,13 +151,9 @@
if type(force) != bool:
raise RelaxBoolError, ('force flag', force)
- # Format.
- if type(format) != str:
- raise RelaxStrError, ('format', format)
-
# Compression type.
if type(compress_type) != int:
raise RelaxIntError, ('compression type', compress_type)
# Execute the functional code.
- results.write(file=file, directory=dir, force=force, format=format,
compress_type=compress_type)
+ bmrb.write(file=file, directory=dir, force=force,
compress_type=compress_type)
r7043 - in /branches/bmrb/prompt: __init__.py bmrb.py