Author: bugman
Date: Wed Oct 1 19:44:35 2014
New Revision: 26119
URL: http://svn.gna.org/viewcvs/relax?rev=26119&view=rev
Log:
Expanded the Structure.test_delete_atom system test.
This is to show that the structure.write_pdb user function fails after a call
to the
structure.delete user function to delete individual atoms.
Modified:
trunk/test_suite/system_tests/structure.py
Modified: trunk/test_suite/system_tests/structure.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/test_suite/system_tests/structure.py?rev=26119&r1=26118&r2=26119&view=diff
==============================================================================
--- trunk/test_suite/system_tests/structure.py (original)
+++ trunk/test_suite/system_tests/structure.py Wed Oct 1 19:44:35 2014
@@ -23,6 +23,7 @@
from math import sqrt
from numpy import array, float64, zeros
from os import sep
+from re import search
import sys
from tempfile import mkdtemp, mktemp
@@ -2644,6 +2645,73 @@
self.assertEqual(mol.z[i], data[i][5])
self.assertEqual(mol.bonded[i], data[i][7])
+ # Output PDB to stdout to help in debugging.
+ self.interpreter.structure.write_pdb(file=sys.stdout)
+
+ # Write out the file.
+ self.tmpfile = mktemp() + '.pdb'
+ self.interpreter.structure.write_pdb(self.tmpfile)
+
+ # Read the contents of the file.
+ file = open(self.tmpfile)
+ lines = file.readlines()
+ file.close()
+
+ # Check the CONECT records.
+ print("\nChecking CONECT records from the structure.write user
function:")
+ connected = [
+ [ 0, 1],
+ [ 1, 0],
+ [ 2, 3],
+ [ 3, 2],
+ [ 4, 5],
+ [ 5, 4],
+ [ 7, 8],
+ [ 8, 7],
+ [ 9, 10],
+ [10, 9],
+ [11, 12],
+ [12, 11],
+ [13, 14],
+ [14, 13],
+ [15, 16],
+ [16, 15],
+ [17, 18],
+ [18, 17],
+ [19, 20],
+ [20, 19],
+ [21, 22],
+ [22, 21],
+ [23, 24],
+ [24, 23],
+ [25, 26],
+ [26, 25],
+ [27, 28],
+ [28, 27],
+ [30, 31],
+ [31, 30],
+ [32, 33],
+ [33, 32],
+ [34, 35],
+ [35, 34]
+ ]
+ i = 0
+ for line in lines:
+ # Not a CONECT record.
+ if not search('^CONECT', line):
+ continue
+
+ # Debugging printout.
+ sys.stdout.write(line)
+
+ # Split up the line.
+ row = line.split()
+
+ # Check and increment.
+ self.assertEqual(int(row[1]), connected[i][0]+1)
+ self.assertEqual(int(row[2]), connected[i][1]+1)
+ i += 1
+
def test_delete_empty(self):
"""Test the deletion of non-existent structural data."""
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