Author: bugman
Date: Fri Dec 5 21:17:18 2008
New Revision: 8159
URL: http://svn.gna.org/viewcvs/relax?rev=8159&view=rev
Log:
Merged revisions 8150-8157 via svnmerge from
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/1.3
........
r8152 | semor | 2008-12-05 20:42:50 +0100 (Fri, 05 Dec 2008) | 12 lines
Changed the generate_spin_id_data_array() arguments.
This follows a post by Ed at:
https://mail.gna.org/public/relax-devel/2008-12/msg00032.html
(# Message-id:
<7f080ed10812051130k7440d48cpf2902ca38dc5786f@xxxxxxxxxxxxxx>)
Different arguments had been set in the idea of implementing complete
automation for field
recognition for the generic file format... This might be implemented at a
higher level as discussed
in a thread started at :
https://mail.gna.org/public/relax-devel/2008-12/msg00029.html
(Message-id: <1228504156.9116.6.camel@localhost>)
........
r8154 | bugman | 2008-12-05 20:51:38 +0100 (Fri, 05 Dec 2008) | 3 lines
Added a missing RelaxError import.
........
r8155 | bugman | 2008-12-05 21:11:38 +0100 (Fri, 05 Dec 2008) | 3 lines
Implemented the interface of the noe.read() user function.
........
r8156 | bugman | 2008-12-05 21:13:15 +0100 (Fri, 05 Dec 2008) | 3 lines
Missing import.
........
r8157 | bugman | 2008-12-05 21:14:41 +0100 (Fri, 05 Dec 2008) | 3 lines
Fixes for 2 of the noe.read() user function arg unit tests.
........
Modified:
branches/bmrb/ (props changed)
branches/bmrb/generic_fns/spectrum.py
branches/bmrb/prompt/noe.py
branches/bmrb/test_suite/unit_tests/_prompt/test_noe.py
Propchange: branches/bmrb/
------------------------------------------------------------------------------
--- svnmerge-integrated (original)
+++ svnmerge-integrated Fri Dec 5 21:17:18 2008
@@ -1,1 +1,1 @@
-/1.3:1-8149
+/1.3:1-8157
Modified: branches/bmrb/generic_fns/spectrum.py
URL:
http://svn.gna.org/viewcvs/relax/branches/bmrb/generic_fns/spectrum.py?rev=8159&r1=8158&r2=8159&view=diff
==============================================================================
--- branches/bmrb/generic_fns/spectrum.py (original)
+++ branches/bmrb/generic_fns/spectrum.py Fri Dec 5 21:17:18 2008
@@ -468,7 +468,7 @@
print ' ' + `res_num`, h_name, x_name, intensity
# Generate the spin identification string.
- spin_id = generate_spin_id_data_array(data=line, mol_name_col=None,
res_num_col=1, res_name_col=None, spin_num_col=None, spin_name_col=None)
+ spin_id = generate_spin_id_data_array(data=line,
mol_name_col=mol_name_col, res_num_col=res_num_col,
res_name_col=res_name_col, spin_num_col=spin_num_col,
spin_name_col=spin_name_col)
# Return the data.
return h_name, x_name, spin_id, intensity
Modified: branches/bmrb/prompt/noe.py
URL:
http://svn.gna.org/viewcvs/relax/branches/bmrb/prompt/noe.py?rev=8159&r1=8158&r2=8159&view=diff
==============================================================================
--- branches/bmrb/prompt/noe.py (original)
+++ branches/bmrb/prompt/noe.py Fri Dec 5 21:17:18 2008
@@ -29,7 +29,7 @@
# relax module imports.
import help
-from relax_errors import RelaxStrError
+from relax_errors import RelaxNoneIntError, RelaxNoneStrError, RelaxStrError
from specific_fns.setup import noe_obj
@@ -44,6 +44,94 @@
# Place relax in the class namespace.
self.__relax__ = relax
+
+
+ def read(self, file=None, dir=None, proton1_col=None, proton2_col=None,
lower_col=None, upper_col=None, sep=None):
+ """Read NOESY or ROESY constraints from a file.
+
+ Keyword Arguments
+ ~~~~~~~~~~~~~~~~~
+
+ file: The name of the file containing the relaxation data.
+
+ dir: The directory where the file is located.
+
+ proton1_col: The column containing the first proton of the NOE or
ROE cross peak.
+
+ proton2_col: The column containing the second proton of the NOE or
ROE cross peak.
+
+ lower_col: The column containing the lower NOE bound.
+
+ upper_col: The column containing the upper NOE bound.
+
+ sep: The column separator (the default is white space).
+
+
+ Description
+ ~~~~~~~~~~~
+
+ This function can automatically determine the format of the file,
for example Xplor
+ formatted constraint files. A generically formatted file is also
supported if it contains
+ minimally four columns with the two proton names and the upper and
lower bounds, as
+ specified by the *_col arguments.
+
+
+ Examples
+ ~~~~~~~~
+
+ To read the Xplor formatted constraint file 'NOE.xpl', type one of:
+
+ relax> noe.read('NOE.xpl')
+ relax> noe.read(file='NOE.xpl')
+
+
+ To read the generic formatted file 'noes', type one of:
+
+ relax> noe.read(file='NOE.xpl', proton1_col=0, proton2_col=1,
lower_col=2, upper_col=3)
+ """
+
+ # Function intro text.
+ if self.__relax__.interpreter.intro:
+ text = sys.ps3 + "noe.read("
+ text = text + "file=" + `file`
+ text = text + ", dir=" + `dir`
+ text = text + ", proton1_col=" + `proton1_col`
+ text = text + ", proton2_col=" + `proton2_col`
+ text = text + ", lower_col=" + `lower_col`
+ text = text + ", upper_col=" + `upper_col`
+ text = text + ", sep=" + `sep` + ")"
+ print text
+
+ # The file name.
+ if type(file) != str:
+ raise RelaxStrError, ('file', file)
+
+ # Directory.
+ if dir != None and type(dir) != str:
+ raise RelaxNoneStrError, ('directory name', dir)
+
+ # First proton column.
+ if proton1_col != None and type(proton1_col) != int:
+ raise RelaxNoneIntError, ('first proton column', proton1_col)
+
+ # Second proton column.
+ if proton2_col != None and type(proton2_col) != int:
+ raise RelaxNoneIntError, ('second proton column', proton2_col)
+
+ # Lower bound column.
+ if lower_col != None and type(lower_col) != int:
+ raise RelaxNoneIntError, ('lower bound column', lower_col)
+
+ # Upper bound column.
+ if upper_col != None and type(upper_col) != int:
+ raise RelaxNoneIntError, ('upper bound column', upper_col)
+
+ # Column separator.
+ if sep != None and type(sep) != str:
+ raise RelaxNoneStrError, ('column separator', sep)
+
+ # Execute the functional code.
+ noe.read(frq=frq, file=file, dir=dir, proton1_col=proton1_col,
proton2_col=proton2_col, lower_col=lower_col, upper_col=upper_col, sep=sep)
def spectrum_type(self, spectrum_type=None, spectrum_id=None):
Modified: branches/bmrb/test_suite/unit_tests/_prompt/test_noe.py
URL:
http://svn.gna.org/viewcvs/relax/branches/bmrb/test_suite/unit_tests/_prompt/test_noe.py?rev=8159&r1=8158&r2=8159&view=diff
==============================================================================
--- branches/bmrb/test_suite/unit_tests/_prompt/test_noe.py (original)
+++ branches/bmrb/test_suite/unit_tests/_prompt/test_noe.py Fri Dec 5
21:17:18 2008
@@ -25,7 +25,7 @@
# relax module imports.
from prompt.noe import Noe
-from relax_errors import RelaxBoolError, RelaxNoneIntError,
RelaxNoneStrError, RelaxStrError
+from relax_errors import RelaxBoolError, RelaxIntError, RelaxNoneIntError,
RelaxNoneStrError, RelaxStrError
# Unit test imports.
from data_types import DATA_TYPES
@@ -97,11 +97,11 @@
# Loop over the data types.
for data in DATA_TYPES:
# Catch the int and bin arguments, and skip them.
- if data[0] == 'int' or data[0] == 'bin':
+ if data[0] == 'None' or data[0] == 'int' or data[0] == 'bin':
continue
# The argument test.
- self.assertRaises(RelaxIntError, self.noe_fns.read, file='noes',
lower_col=data[1])
+ self.assertRaises(RelaxNoneIntError, self.noe_fns.read,
file='noes', lower_col=data[1])
def test_read_argfail_upper_col(self):
@@ -110,11 +110,11 @@
# Loop over the data types.
for data in DATA_TYPES:
# Catch the int and bin arguments, and skip them.
- if data[0] == 'int' or data[0] == 'bin':
+ if data[0] == 'None' or data[0] == 'int' or data[0] == 'bin':
continue
# The argument test.
- self.assertRaises(RelaxIntError, self.noe_fns.read, file='noes',
upper_col=data[1])
+ self.assertRaises(RelaxNoneIntError, self.noe_fns.read,
file='noes', upper_col=data[1])
def test_read_argfail_sep(self):
r8159 - in /branches/bmrb: ./ generic_fns/spectrum.py prompt/noe.py test_suite/unit_tests/_prompt/test_noe.py