Author: bugman
Date: Thu Apr 4 15:14:11 2013
New Revision: 19354
URL: http://svn.gna.org/viewcvs/relax?rev=19354&view=rev
Log:
Created the lib.software.sparky.write_list() function and associated unit
test.
This will be used to create simple Sparky .list files.
Added:
trunk/test_suite/unit_tests/_lib/_software/test_sparky.py
Modified:
trunk/lib/software/sparky.py
Modified: trunk/lib/software/sparky.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/lib/software/sparky.py?rev=19354&r1=19353&r2=19354&view=diff
==============================================================================
--- trunk/lib/software/sparky.py (original)
+++ trunk/lib/software/sparky.py Thu Apr 4 15:14:11 2013
@@ -107,3 +107,72 @@
# Return the data.
return data
+
+
+def write_list(file_prefix=None, dir=None, res_names=None, res_nums=None,
atom1_names=None, atom2_names=None, w1=None, w2=None, data_height=None,
force=True):
+ """Create a Sparky .list file.
+
+ @keyword file_prefix: The base part of the file name without the .list
extension.
+ @type file_prefix: str
+ @keyword dir: The directory to place the file in.
+ @type dir: str or None
+ @keyword res_names: The residue name list for each peak entry.
+ @type res_names: list of str
+ @keyword res_nums: The residue number list for each peak entry.
+ @type res_nums: list of int
+ @keyword atom1_names: The atom name list for w1 for each peak entry.
+ @type atom1_names: list of str
+ @keyword atom2_names: The atom name list for w2 for each peak entry.
+ @type atom2_names: list of str
+ @keyword w1: The w1 chemical shift list in ppm for each peak
entry.
+ @type w1: list of float
+ @keyword w2: The w2 chemical shift list in ppm for each peak
entry.
+ @type w2: list of float
+ @keyword data_height: The optional data height list for each peak
entry.
+ @type data_height: None or list of float
+ @keyword force: A flag which if True will cause any pre-existing
files to be overwritten.
+ @type force: bool
+ """
+
+ # Checks.
+ N = len(w1)
+ if len(res_names) != N:
+ raise RelaxError("The %s residue names does not match the %s number
of entries." % (len(res_names), N))
+ if len(res_nums) != N:
+ raise RelaxError("The %s residue numbers does not match the %s
number of entries." % (len(res_nums), N))
+ if len(atom1_names) != N:
+ raise RelaxError("The %s w1 atom names does not match the %s number
of entries." % (len(atom1_names), N))
+ if len(atom2_names) != N:
+ raise RelaxError("The %s w2 atom names does not match the %s number
of entries." % (len(atom2_names), N))
+ if len(w1) != N:
+ raise RelaxError("The %s w1 chemical shifts does not match the %s
number of entries." % (len(w1), N))
+ if len(w2) != N:
+ raise RelaxError("The %s w2 chemical shifts does not match the %s
number of entries." % (len(w2), N))
+ if data_height and len(data_height) != N:
+ raise RelaxError("The %s data heights does not match the %s number
of entries." % (len(data_height), N))
+
+ # Printout.
+ print("Creating the Sparky list file.")
+
+ # Open the file.
+ if isinstance(file_prefix, str):
+ file = open_write_file(file_name=file_prefix+".list", dir=dir,
force=force)
+ else:
+ file = file_prefix
+
+ # The header.
+ file.write("%17s %10s %10s" % ("Assignment ", "w1 ", "w2 "))
+ if data_height != None:
+ file.write(" %12s" % "Data Height")
+ file.write("\n\n")
+
+ # The data.
+ for i in range(N):
+ # Generate the assignment.
+ assign = "%s%i%s-%s" % (res_names[i], res_nums[i], atom1_names[i],
atom2_names[i])
+
+ # Write out the line.
+ file.write("%17s %10.3f %10.3f" % (assign, w1[i], w2[i]))
+ if data_height != None:
+ file.write(" %12i" % data_height[i])
+ file.write("\n")
Added: trunk/test_suite/unit_tests/_lib/_software/test_sparky.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/test_suite/unit_tests/_lib/_software/test_sparky.py?rev=19354&view=auto
==============================================================================
--- trunk/test_suite/unit_tests/_lib/_software/test_sparky.py (added)
+++ trunk/test_suite/unit_tests/_lib/_software/test_sparky.py Thu Apr 4
15:14:11 2013
@@ -1,0 +1,69 @@
+###############################################################################
+#
#
+# Copyright (C) 2013 Edward d'Auvergne
#
+#
#
+# This file is part of the program relax (http://www.nmr-relax.com).
#
+#
#
+# This program 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 3 of the License, or
#
+# (at your option) any later version.
#
+#
#
+# This program 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 this program. If not, see <http://www.gnu.org/licenses/>.
#
+#
#
+###############################################################################
+
+# Python module imports.
+from numpy import array, eye, float64, zeros
+from sys import stdout
+from unittest import TestCase
+
+# relax module imports.
+from lib.io import DummyFileObject
+from lib.software.sparky import write_list
+
+
+class Test_sparky(TestCase):
+ """Unit tests for the lib.software.sparky relax module."""
+
+ def test_write_list(self):
+ """Test the lib.software.sparky.write_list() function."""
+
+ # The data.
+ res_names = ['LEU', 'GLY', 'SER', 'MET', 'TRP', 'TRP', 'ASN']
+ res_nums = [3, 4, 5, 6, 40, 40, 55]
+ atom1_names = ['N', 'N', 'N', 'N', 'N', 'NE1', 'N']
+ atom2_names = ['HN', 'HN', 'HN', 'HN', 'HN', 'HE1', 'HN']
+ w1 = [122.454, 111.978, 115.069, 120.910, 123.335, 130.204, 116.896]
+ w2 = [8.397, 8.720, 8.177, 8.813, 8.005, 10.294, 7.468]
+ heights = [2535, 5050, 51643, 53663, -65111, -181131, -105322]
+
+ # The result.
+ file_data = [
+ ' Assignment w1 w2 Data Height\n',
+ '\n',
+ ' LEU3N-HN 122.454 8.397 2535\n',
+ ' GLY4N-HN 111.978 8.720 5050\n',
+ ' SER5N-HN 115.069 8.177 51643\n',
+ ' MET6N-HN 120.910 8.813 53663\n',
+ ' TRP40N-HN 123.335 8.005 -65111\n',
+ ' TRP40NE1-HE1 130.204 10.294 -181131\n',
+ ' ASN55N-HN 116.896 7.468 -105322\n'
+ ]
+
+ # Write the data out.
+ file = DummyFileObject()
+ write_list(file_prefix=file, res_names=res_names, res_nums=res_nums,
atom1_names=atom1_names, atom2_names=atom2_names, w1=w1, w2=w2,
data_height=heights)
+
+ # Check the file data.
+ lines = file.readlines()
+ print lines
+ self.assertEqual(len(lines), len(file_data))
+ for i in range(len(lines)):
+ self.assertEqual(lines[i], file_data[i])
r19354 - in /trunk: lib/software/sparky.py test_suite/unit_tests/_lib/_software/test_sparky.py