Author: bugman
Date: Wed Feb 20 12:11:58 2013
New Revision: 18522
URL: http://svn.gna.org/viewcvs/relax?rev=18522&view=rev
Log:
Created unit tests for the generic_fns.structure.pdb_write module.
This currently covers the atom(), helix() and sheet() functions (the last 2
are not yet
implemented).
Added:
trunk/test_suite/unit_tests/_generic_fns/_structure/test_pdb_write.py
- copied, changed from r18519,
trunk/test_suite/unit_tests/_generic_fns/_structure/test_pdb_read.py
Modified:
trunk/test_suite/unit_tests/_generic_fns/_structure/__init__.py
Modified: trunk/test_suite/unit_tests/_generic_fns/_structure/__init__.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/test_suite/unit_tests/_generic_fns/_structure/__init__.py?rev=18522&r1=18521&r2=18522&view=diff
==============================================================================
--- trunk/test_suite/unit_tests/_generic_fns/_structure/__init__.py (original)
+++ trunk/test_suite/unit_tests/_generic_fns/_structure/__init__.py Wed Feb
20 12:11:58 2013
@@ -1,6 +1,6 @@
###############################################################################
#
#
-# Copyright (C) 2008 Edward d'Auvergne
#
+# Copyright (C) 2008-2013 Edward d'Auvergne
#
#
#
# This file is part of the program relax (http://www.nmr-relax.com).
#
#
#
@@ -20,7 +20,11 @@
###############################################################################
-__all__ = ['test_api_base',
- 'test__init__',
- 'test_internal',
- 'test_scientific']
+__all__ = [
+ 'test_api_base',
+ 'test__init__',
+ 'test_internal',
+ 'test_pdb_read',
+ 'test_pdb_write',
+ 'test_scientific'
+]
Copied: trunk/test_suite/unit_tests/_generic_fns/_structure/test_pdb_write.py
(from r18519,
trunk/test_suite/unit_tests/_generic_fns/_structure/test_pdb_read.py)
URL:
http://svn.gna.org/viewcvs/relax/trunk/test_suite/unit_tests/_generic_fns/_structure/test_pdb_write.py?p2=trunk/test_suite/unit_tests/_generic_fns/_structure/test_pdb_write.py&p1=trunk/test_suite/unit_tests/_generic_fns/_structure/test_pdb_read.py&r1=18519&r2=18522&rev=18522&view=diff
==============================================================================
--- trunk/test_suite/unit_tests/_generic_fns/_structure/test_pdb_read.py
(original)
+++ trunk/test_suite/unit_tests/_generic_fns/_structure/test_pdb_write.py Wed
Feb 20 12:11:58 2013
@@ -20,87 +20,60 @@
###############################################################################
# relax module imports.
-from generic_fns.structure import pdb_read
+from generic_fns.structure import pdb_write
+from relax_io import DummyFileObject
from test_suite.unit_tests.base_classes import UnitTestCase
-class Test_pdb_read(UnitTestCase):
- """Unit tests for the functions of the 'generic_fns.structure.pdb_read'
module."""
+class Test_pdb_write(UnitTestCase):
+ """Unit tests for the functions of the 'generic_fns.structure.pdb_write'
module."""
def test_atom(self):
- """Test the pdb_read.atom() function."""
+ """Test the pdb_write.atom() function."""
- # Parse a PDB record.
- record = pdb_read.atom('ATOM 158 CG GLU 11 9.590
-1.041 -11.596 1.00 0.00 C')
+ # A dummy file to write to.
+ file = DummyFileObject()
- # Test the elements.
- self.assertEqual(record[0], 'ATOM')
- self.assertEqual(record[1], 158)
- self.assertEqual(record[2], 'CG')
- self.assertEqual(record[3], None)
- self.assertEqual(record[4], 'GLU')
- self.assertEqual(record[5], None)
- self.assertEqual(record[6], 11)
- self.assertEqual(record[7], None)
- self.assertEqual(record[8], 9.59)
- self.assertEqual(record[9], -1.041)
- self.assertEqual(record[10], -11.596)
- self.assertEqual(record[11], 1.0)
- self.assertEqual(record[12], 0.0)
- self.assertEqual(record[13], 'C')
- self.assertEqual(record[14], None)
+ # Create the PDB record.
+ pdb_write.atom(file, serial=158, name='CG', res_name='GLU',
res_seq='11', x=9.59, y=-1.041, z=-11.596, occupancy=1.0, temp_factor=0.0,
element='C')
+
+ # Test the record.
+ records = file.readlines()
+ actual = 'ATOM 158 CG GLU 11 9.590 -1.041 -11.596
1.00 0.00 C \n'
+ print(repr(records[0]))
+ print(repr(actual))
+ self.assertEqual(records[0], actual)
def test_helix(self):
- """Test the pdb_read.helix() function."""
+ """Test the pdb_write.helix() function."""
- # Parse a PDB record (from the 1UBQ PDB file).
- record = pdb_read.helix('HELIX 1 H1 ILE A 23 GLU A 34 1
12 ')
+ # A dummy file to write to.
+ file = DummyFileObject()
- # Test the elements.
- self.assertEqual(record[0], 'HELIX')
- self.assertEqual(record[1], 1)
- self.assertEqual(record[2], 'H1')
- self.assertEqual(record[3], 'ILE')
- self.assertEqual(record[4], 'A')
- self.assertEqual(record[5], 23)
- self.assertEqual(record[6], None)
- self.assertEqual(record[7], 'GLU')
- self.assertEqual(record[8], 'A')
- self.assertEqual(record[9], 34)
- self.assertEqual(record[10], None)
- self.assertEqual(record[11], 1)
- self.assertEqual(record[12], None)
- self.assertEqual(record[13], 12)
+ # Create the PDB record.
+ pdb_write.helix(file, ser_num=1, helix_id='H1', init_res_name='ILE',
init_chain_id='A', init_seq_id=23, init_icode=None, end_res_name='GLU',
end_chain_id='A', end_seq_num=34, end_icode=None, helix_class=1,
comment=None, length=12)
+
+ # Test the record.
+ records = file.readlines()
+ actual = 'HELIX 1 H1 ILE A 23 GLU A 34 1
12 \n'
+ print(repr(records[0]))
+ print(repr(actual))
+ self.assertEqual(records[0], actual)
def test_sheet(self):
- """Test the pdb_read.sheet() function."""
+ """Test the pdb_write.sheet() function."""
- # Parse a PDB record (from the 1UBQ PDB file).
- record = pdb_read.sheet('SHEET 1 BET 5 GLY A 10 VAL A 17 0
')
+ # A dummy file to write to.
+ file = DummyFileObject()
- # Test the elements.
- self.assertEqual(record[0], 'SHEET')
- self.assertEqual(record[1], 1)
- self.assertEqual(record[2], 'BET')
- self.assertEqual(record[3], 5)
- self.assertEqual(record[4], 'GLY')
- self.assertEqual(record[5], 'A')
- self.assertEqual(record[6], 10)
- self.assertEqual(record[7], None)
- self.assertEqual(record[8], 'VAL')
- self.assertEqual(record[9], 'A')
- self.assertEqual(record[10], 17)
- self.assertEqual(record[11], None)
- self.assertEqual(record[12], 0)
- self.assertEqual(record[13], None)
- self.assertEqual(record[14], None)
- self.assertEqual(record[15], None)
- self.assertEqual(record[16], None)
- self.assertEqual(record[17], None)
- self.assertEqual(record[18], None)
- self.assertEqual(record[19], None)
- self.assertEqual(record[20], None)
- self.assertEqual(record[21], None)
- self.assertEqual(record[22], None)
+ # Create the PDB record.
+ pdb_write.sheet(file, strand=1, sheet_id='BET', num_strands=5,
init_res_name='GLY', init_chain_id='A', init_seq_num=10, init_icode=None,
end_res_name='VAL', end_chain_id='A', end_seq_num=17, end_icode=None,
sense=0, cur_atom=None, cur_res_name=None, cur_chain_id=None,
cur_res_seq=None, cur_icode=None, prev_atom=None, prev_res_name=None,
prev_chain_id=None, prev_res_seq=None, prev_icode=None)
+
+ # Test the record.
+ records = file.readlines()
+ actual = 'SHEET 1 BET 5 GLY A 10 VAL A 17 0
\n'
+ print(repr(records[0]))
+ print(repr(actual))
+ self.assertEqual(records[0], actual)
r18522 - in /trunk/test_suite/unit_tests/_generic_fns/_structure: __init__.py test_pdb_write.py